Days Gone By
by KageOkami-Kogo
Summary: Lincoln Lee stands by the redheaded Olivia Dunham, watching his old universe disappear. This is the story of how Lincoln adapted to the other side, and how he became the confident man we all knew he could become. And, of course, the story of how he gave up his glasses. Slow building Amber!Lincoln x Red!Olivia, post 4x20. Being Fringe means weird cases abound! ON HIATUS!
1. Processing

**Days Gone By**

_First there was the one who challenged_

_All my dreams and all my balance_

_She could never be as good as you_

_You could be my unintended_

_Choice to live my life extended_

_~Muse – Unintended_

**Disclaimer: **I do not own Fringe, and I do not own the characters, but I do own this plot for this fan-based story.

**A/N:** I figured my little come-back to writing fanfiction, even if it's in a limited bases for now, would be with an old flame of mine! Fringe! More specifically Leeham! I'll always miss Alt!Lincoln, and I was very sad by his death... but I'm not the type of person to completely change canon like that. Anyway, "our" Lincoln _is _still Lincoln, as I mentioned before in an AN in my story "Substitute", so I figured with enough exposure to "over there" and Fringe Division, he'd sort of become like a blend between "our" universe and "over there"!

This is the story of how "our" Lincoln adapted to the "other" side and ended up being the confident person we saw in the season 5 episode called "Liberty". Starts out exactly where the bridge collapse leaves them off. Just so you know, I have classes and work so I don't have a whole lot of time on my hands to update, so expect an update at least twice or three times a week or so, maybe more depending on how fired-up I am.

Please enjoy!

**Rating:** T – but that _may _change in the future. If it does, I'll put a warning at the top of the chapter so you can skip it if you so chose to do so.

**Inspired by music:** Muse – Unintended

* * *

They say the brain processes images to one tenth of a second. They also say the brain is made up of about a hundred billion cells, all interlinked and working together. It is much like they say the universe is split up into interlinked alternates, all woven together like a tapestry. That being said, the vast amount of networked neurons and cells in the brain allow us to process about twenty billion calculations of information at any time.

But this?

This was just almost too much to process. First there was just one universe, one thread in the intricately woven pattern of existence. Acknowledging that there are many of us, making different choices, occupying the same space, all happening at once, in itself was a huge leap. But to then accept that one of those universes had been figuratively and then literally linked together by a machine created to destroy or give life – depending on who you asked – to heal the other? Well, it would be enough to make anyone's brain, despite how efficient it was, to fry in a split second!

But at that very moment, the red-headed Olivia Dunham couldn't be bothered by that. To her, all those bits of trivia and facts were useless drabble. To her, staring at her other self, remembering to just "keep looking up" made her smile, and at the same time, gave her a pang of regret, guilt for what she had done to her alternate. It also made her a little sad to see her go. She thought of Walter then, how different he was to the Secretary of Defense that she had met a handful of times now. This Walter was unpredictable, wild, and oddly charming. She regretted fooling him as well, as she had come to enjoy spending time with him. She would miss him. She would miss all of them! Astrid with her care-free, cheerful and optimistic attitude to the world, and even Gene! That cow that Walter kept, that seemed to be able to read minds and moo at just the right moments. She would, she would miss them.

And then there was the Secretary's son. Olivia hadn't met Peter before, she didn't think, but she felt something strange when she was around him. The closest thing she could describe it as was that he felt right and at the same time wrong. She knew he was from a different "timeline", as opposed to a different universe like they had all thought at first, but that wasn't it. He didn't feel right in her universe... which was ironic since a different version of him belonged there, and in that different timeline so did he. At the same time, she felt the oddest sense of guilt when around him as well. She could not recall ever doing anything to him to inspire that sort of feeling though, but at moments it was as though she felt like she knew him at one time. Then again, she was part of Fringe Division. So who knew?

Ah, but that just left one other person. He had just told her that he would stick around, making the excuse that he could "help" them. She could not deny that learning that he would be staying, pulled away from his own realm of existence, his own universe, to help her– to help _Fringe Division, _was a great source of comfort for her. She had been partners with his alternate for close to a decade it seemed, and had been at his funeral – the thought making her eyes burn for a moment – but she couldn't have imagined that she would have formed a bond with this man, this man standing right by her side. But then, it made complete sense. As different as they seemed, they were essentially the same person, right?

In a brilliant yet oddly fuzzy flash, the other universe, the 'prime' universe as some had called it, vanished. It took Olivia by surprise for a moment, how quickly it had happened. A fear so terrible it made her immobile gripped her heart for a second. Was _he _next to her still? She could not bring herself to look. How could he have just gone with them instead of disappearing into his rightful universe with the rest? They had parted onto their own "sides" as more of a symbol than anything else. Surely his own universe would have pulled him in, right?

And then she heard a sound she would have never thought she would be so happy to hear. A soft sigh, a soft breath of a man still very much in that universe with her. Turning to look at him, she noticed the reason for his almost weary exhale. He looked lost, troubled. Feeling guilt once again for having such selfish thoughts, Olivia hadn't stopped to consider what _he _could be feeling at that moment. After all, he _had _just lost his entire universe with everything he had ever known. Unable to resist the urge, Olivia placed her hand on her friend's shoulder, hoping to comfort him, or at least show him that she was there and would support him.

Lincoln Lee had been so deep in thought, so lost in wondering if he had made a mistake asking Walter to do this for him, that he had forgotten where he was for a second. Feeling the hand on his shoulder made him jump inwardly. He turned slightly to look at the beaming smile of the red-head. Suddenly the words he had told Peter came to mind. His heart _had _found its home. A wave of relief, of the feeling that he was in the right place, by her side, filled the hole that he hadn't noticed had been in his heart. His old partner had spoken to him about finding what tethered him to the world, well, he now knew he had found his link. Lincoln could see the questions in her eyes, and hoped his reassuring smile would let her know that he planned to share answers soon. Olivia hadn't missed the look he gave her and nodded in acceptance.

Footsteps walking toward them drew them to the attention of Secretary Bishop. In stark contrast to the lively and eccentric Walter they knew, Bishop was somber and serious, his features firm and steps assured. "Secretary." Lincoln and Olivia both acknowledged him with a polite nod, and slightly straighter postures.

"Agents," Bishop greeted back. He turned his attention to Lincoln, his brows meeting in a critical stare. "Agent Lee, I assume my alternate had a hand in your continued stay?"

"Yes, Sir." Lincoln fidgeted slightly under the older man's gaze.

Bishop thought for a moment. If this young man was anything like his previous version, he would develop into an important asset to Fringe Division. It would make sense to allow him to remain. Unfortunately, there was very little known about _this _Lincoln Lee and he no doubt had had different training. In any case, they would have to deal with processing him soon enough anyway. "I will need a full report on that as soon as possible. Now, since you are a new and permanent fixture to this universe, we will now of course have to decide what to do with you."

"I'm sorry – we?" Lincoln questioned.

"I must inform my superiors, including the president, that there is now another Lincoln Lee. If you are going to continue to serve Fringe Division, steps must be taken to avoid confusion. You have people you report to, and so do I," Bishop explained. "I hope you understand that you can never go back to your universe. I hope you made the right decision, son," Bishop added in a softer tone. It was moments like this that anyone would be able to see there was still a kind man, just like Walter from the other universe, deep inside of him, even though his exterior was always hard and business-like. "We'll be watching you, Agent Lee. I hope you understand that you're still an unknown variable to us. Until you can be tested, you will need to be _escorted."_

"Am I a prisoner?" Lincoln asked, thankful that his voice didn't waver. He had no illusions that his choice to remain in this universe wouldn't come with consequences. He just hoped they wouldn't immediately dismiss him as just a "copy" or "replacement" for the Lincoln Lee that they had lost.

Bishop's lips quirked into a very fleeting smile. "No, you're not a prisoner. However, as this is sudden and we can not risk you being seen without proper identification. We will have to have you stay at Fringe headquarters for the time being. There are cells with beds that you can use. You are not a prisoner, but for the time being that will have to do, understand?"

"Yes sir, I understand," Lincoln nodded, pushing his glasses up the bridge of his nose nervously.

Bishop noticed Agent Dunham give the young agent a reassuring smile. "Alright then. I will leave you in Agent Dunham's capable hands. Come Agent Farnsworth, I need your assistance with some calculations. We have a bit of an amber mess to continue cleaning up," Bishop turned and lead the other agents through the gate, leaving agent Dunham to him.

Olivia turned to Lincoln and grinned. "So!" She began, giving him an expectant look.

Lincoln knew what she wanted to know. "How did I stay?" He figured if she was as inquisitive as her alternate, she'd want to know everything. He knew he would.

"Yep!" Olivia answered with a slight eager rock on her heels, just shy of popping the P.

"Do you remember when Walter told us that each universe vibrated at different frequencies?" He began. When Olivia nodded, he continued. "Well, as you know my... my _former_ universe, vibrated at a C, this one at a G... he used the same process David Jones used to change peoples' frequency signatures to change mine. That was the only way I would be able to go with you- I mean to stay in this universe," he amended quickly. He could feel his ears burning and just hoped he wasn't blushing too much.

Olivia studied him for a moment, the smile never having left her face. "Well I'm glad you're here," she told him honestly.

Lincoln relaxed and smiled back, "me too". Despite the troubles that would surely come his way, despite not having anything, despite this being incredibly risky, depending on whether or not who he longed to be with reciprocated the feeling, he truly was happy he made this decision. Back "home", he didn't feel needed or wanted anymore. Sure, Broyles had said that he was needed, but he wasn't really. Lincoln had been an agent, but there were plenty of agents there, he was just an extra warm body to fill the room and do some paperwork – he wouldn't _really _be needed. Here though... here he felt like he belonged a lot more than in his birth universe. Whether it was because he actually had someone who needed his support, or because he was "filling in" for someone who had "left", it didn't matter to him.

At this very moment, this was right.

After the rather silent ride back to Fringe headquarters, Lincoln was directed to a holding cell. Olivia approached him once more, glancing around the cell in distaste. The walls were a dark color and bare, the 'bed' was a sheet of thick metal, there was a steel table and uncomfortable looking chairs by them, and the place smelled of cleaning fluids trying to mask blood and sweat. "I'll see about getting you some basic comforts," she assured him.

Lincoln glanced around and shrugged. "It's fine... I don't need much," he told her.

"You could at least use a blanket and some pillows," Olivia's nose scrunched at the visage of the cold steel horribly uncomfortable looking excuse for a bed. "You're not a prisoner, so I won't have them treat you like one," she insisted. Just then an armed guard walked over, an apologetic look on his face. "Oh no, no way," she gritted her teeth slightly.

"I'm sorry, but I have orders to watch over Agent Lee," the dark-skinned man said softly. No doubt he had heard the conversation and felt guilty. Not that he'd refuse to obey an order from the Secretary of Defense himself regarding a potential risk.

"Why?" Olivia demanded. She'd be damned if her friend was going to be treated like a common criminal!

"It's fine, Olivia, I get it-" Lincoln began, but was cut off.

"-The hell it's fine!" She snapped at the poor guard, who seemed to shrink a little.

"I'm sorry, ma'am. Secretary Bishop doesn't want to take any chances until he is evaluated..." The guard insisted.

"'Liv..." Lincoln began. This caught Olivia's attention. She glanced at him, her lips quirking into a small smile, momentarily forgetting what she had been angry about. Momentarily. This was the first time she heard this Lincoln call her by her nickname. "It's really okay. I can handle a little supervision for a while. I'll take the 'evaluation' and prove I'm not a threat or anything. Secretary Bishop already told me before that I would be watched, remember?"

Olivia sighed silently and nodded. "Alright, but-" she turned to the guard, "-he is _not _a prisoner, understand?"

"Yes, ma'am, if he needs something we'll get it for him," the guard agreed hurriedly.

"That's not what- ugh, alright whatever," Olivia threw her hands up. If she continued to argue she would just make a simple situation worse than it was. She turned again to Lincoln and smiled a little less upbeat than what was normal for her. "I'll see you tomorrow, okay? 'Pretty sure you'll have a big day ahead of you... get some rest. I'll be back with some blankets."

"Good night, Oli- ...'Liv," Lincoln smiled back, remembering to call her by her nickname. He hadn't missed her happiness to the friendly name. He just hoped he could become as good a friend to her as his alternate had been... or, possibly... maybe... something more, in the future? He hoped he wasn't holding his breath on that. If the... _other _Olivia, hadn't seemed to have much interest in him, and _this _Olivia hadn't seen _her _Lincoln as more than a "shoulder to cry on", then where did _he _stand?

As if to answer, Olivia paused from leaving, looking back over to him one last time. The look she gave him was as though she were making sure that he was really there, that he wasn't a figment of her imagination and not about to disappear. It gave him some hope. They smiled once more at each other before she turned again and walked out. Once she had left, Lincoln closed the door to a crack for more privacy and loosened his tie. With another weary sigh, he sat on the frigid, hard steel slab and leaned back against the wall, his forearm covering his face, thoughts racing.

This was going to be a long new life.

_**TBC...**_

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**End A/N: **There you have it, the first chapter to my new story since one of my other ones were stolen. I hope the new security measures FFNET implemented will ward off more thefts. Anywho, I hope you enjoyed this first chapter! I decided to write this after rewatching all of Fringe recently. I'm not the type of person that usually likes to completely change canon, so I'll try to keep things as in character, including universe-wise, as I can. If you notice anything off, including grammar or spelling, please let me know so I can fix it! That being said, please let me know what you thought of this! I value input, good or bad, immensely! Shout-Outs will be at the bottom!


	2. Homework

**Days Gone By**

**Disclaimer: **I do not own Fringe, and I do not own the characters, but I do own this plot for this fan-based story.

* * *

_The sky was overcast, mirroring the ominous atmosphere surrounding her. Olivia Dunham stood amongst a group of soldiers, by a large black escort van. Beside her, her partner, or perhaps the more accurate description of him would be her _alternate _partner, stood quietly. Olivia tensed, watching her actual partner step through the warehouse door, guiding their new informer. Ice cold fear sent bony tendrils snaking through her chest, gripping her rapidly pounding heart. _

_It was going to happen again! _

_"No, not again..." Olivia spun around, looking for the shooter, but she couldn't see him yet. She turned back and called to her partner. "Lincoln! Get back! There's a shooter!" She yelled, but it was as though he hadn't heard her, he kept approaching. "Lincoln, go back! You're going to be shot! Please!" She felt the sting of tears in her eyes. She turned to her alternate partner and put a hand on his shoulder, shaking him slightly, trying to get his attention... but he didn't respond, he just kept looking ahead, waiting for his double to approach. "Lincoln!" She all but yelled in his ear, but still that did nothing._

_BANG!_

"Lincoln!" Olivia shot up from bed. She did not feel the cold sweat making her sheets stick to her. She did not feel the wildly beating heart against her ribs. She did not feel her fingers cramping as she gripped her tangled sheets tightly. Nor did she feel the hot tears on her cheeks. All she felt was the overwhelming loss and knowledge that what she had was not just a simple dream, but it was a vivid and merciless memory she could not escape from. Covering her face in her hands, she gasped, desperately trying to keep herself from weeping. If she let herself cry now, she would not be able to get out of bed. Besides... she had someone waiting for her back at Fringe headquarters. Wiping angrily at the tears that continued their silent trek down her cheeks, she forced herself to remember that he might not be exactly the same, but her new partner was still in a way the same man. The thought was at least a start, it was enough to help pull herself together and kick the covers off.

Olivia gripped the edge of her dresser for a moment, taking deep breaths and letting them out slowly. After a few minutes she felt a little better. Finally stepping back, she took her clothes that she had set out the night before and went to take a good and hot shower. Once she was cleaned and dressed, she ate a quick breakfast of toast and a piece of fruit and got in her car. The drive to work was silent, no catchy tunes or witty radio programs, she was in no mood for any of that, that morning. The only thing she could think of at the moment was that she needed to help get... Lincoln's... situation straightened out. She kicked herself mentally for tripping over his name.

This is was not the first time she had a morning like this, after her partner's... death. But perhaps because of the fact that this "new" Lincoln would now be permanently staying in her universe, it just served to solidify the fact that... he was still Lincoln, however, he wasn't the same. This in turn made the dreams a lot more potent. She only hoped he was right and it would get easier with time.

Stepping into the building, she took her time approaching the guard. She didn't know how she would react this morning to seeing him. She could usually keep her unfazed act together and pretend everything was just great, but today was an especially difficult morning. Giving the guard her show-me and letting him scan her, she passed the threshold leading to the elevator she needed to take to the main floor. She looked up as someone approached her.

"Hey there, Jerry," Olivia put on her usual bright smile for her coworker. Jerry was the type of guy that even though you made sure to let him know you weren't interested, he went out of his way to try to dazzle you with gifts and complements anyway, in the hopes you'd "change your mind". It wasn't that he wasn't attractive. He was tall, had silky caramel skin, a neatly trimmed goatee, and toned very nicely... but he wasn't what she was looking for, he wasn't what she needed right now... if only she knew what that was.

"Hello, 'Liv!" Jerry smiled warmly. "I uh, got you this..." he grinned, handing her a hot cup of sweet sweet caffeinated... tea. Sure, it wasn't coffee, but if it would help give her a much needed boost, she'd happily take it.

"Thanks, Jer," Olivia offered him a real smile this time, accepting the cup.

"Give 'em hell today," Jerry called as Olivia walked on. Olivia rolled her eyes slightly but lifted her hand in a wave to him and continued around the corner. Stepping onto the elevator, she rode it in silence, thankful there was no one with her that morning. She used the time alone to further collect her thoughts and prepare for the day, as she usually did. When she reached the main floor she was greeted by Astrid, very efficiently informing her that Bishop had stopped by earlier that morning and left some documents and items for Lincoln.

"Thanks, Astrid," Olivia smiled warmly at the eccentric agent.

As she walked to Broyles' old office, Olivia fleetingly wondered what it was that caused this Astrid to be so radically different than the one from the other universe. Noting the stack of papers and folders on the desk, she walked over and lifted the folder sitting on top. Inside was Lincoln's new show-me as well as a few security documents for him to sign. Under the stack of papers she found a few books, some very similar to what she had to study when she had her espionage mission in the other universe. Taking the stack of items in her hand while balancing her cup of tea in the other, she made her way to Lincoln's cell. She nodded to the guard who offered to hold the documents and rapped her knuckles on the metal door. There was a bit of rustling inside but nothing else. She nodded again to the guard, gesturing for him to open the door. Stepping in with the stack of documents again resting on the crook of her arm, she noted that Lincoln had chosen to sleep atop the blankets she had gotten him last night and with his clothes still on. She couldn't blame him, not only was the "bed" extremely uncomfortable, there also wasn't a lot of privacy there. Setting the files and books down on the table in the center of the cell, she tried clearing her throat and then calling him a few times. When he didn't budge, she sighed and walked over to him. Shaking him gently did nothing, so she shook him harder and called him again.

"Wha?" Lincoln jerked awake. His eyes popped open, now alert, looking around wildly until they landed in confusion at the woman standing beside him. For a moment he forgot where he was and why Olivia had red hair... but then he remembered. Somehow, this made him relax.

"It's about time. What? Did someone drug you or something?" Olivia joked, stepping back to let him sit up. She only hoped that wasn't actually true... or else she's have some skulls to bash. Then again, that could be just what she needed that morning! Nothing like a bit of righteous violence to wake you up in the morning! Olivia snorted inwardly at the ridiculous thoughts rattling in her apparently still frazzled mind and turned back to Lincoln when he spoke.

"No," Lincoln yawned into his arm and stretched, grimacing when pain flared throughout his body. "It just wasn't the best night," he elaborated.

"I'm sorry," Olivia began, a guilty look on her face. "Maybe you could..." she bit her lip, unsure if she should offer. "Maybe you'd feel more comfortable at... my apartment?" She kicked herself for sounding so much like a school-girl. It wasn't like she meant anything by that! She simply wanted her new friend to be comfortable!

Lincoln blinked in surprise, silent for a moment before his lips twitched up to a smile. "Unfortunately, I don't think Secretary Bishop would appreciate me disappearing like that and burdening you with my presence," he shrugged, wincing slightly when he did.

"You are _not _a burden," Olivia frowned. "What gave you the idea that you were?" She demanded, crossing her arms, the tea cup all but hanging in the air with how she held it.

Lincoln shifted uneasily a little, unsure how to phrase what he wanted to say without setting her off. "I'm an unexpected addition here. I don't really, well, ..._belong_." Oh he knew the words were ridiculous before he finished saying them, but he felt like he could confide his inner feelings in her, despite only _really _just meeting her a few times.

"That's a load of crap. You've been a huge help to us. You're an awesome agent, Lincoln; you're an asset to the division, not a burden. So quit putting yourself down, okay?" She scolded him.

"Sorry," Lincoln smiled, yawning once more. "So, is that for me?" he asked as he got up to sit over at the table.

"Yep, you have loads of fun ahead of you today! A lot of papers to sign, books to read, and an entire universal culture to assimilate!" She grinned. "Here, I think you'll need this more than me," Olivia set down her untouched but thankfully still hot cup of tea in front of him.

"Thanks," Lincoln said gratefully and took a sip. "Oh," he grimaced, "not coffee..."

"Yeah, sorry buddy, not a whole lot of that going around these days," Olivia shrugged.

Forcing another sip of the drink before setting it down, Lincoln decided to just go ahead and jump right into the papers. "Maybe they should plant coffee been trees in a controlled environment? Like a large greenhouse or something?" He suggested idly, while flipping through the files.

Olivia laughed softly and shook her head. "Oh I wish it were as simple as that. Who knows though, with how much our world has healed already, who's to say there is even still a blight around? Maybe some of the vegetation will start to grow again?" She shrugged. The thought was certainly a pleasant one. The bridge between the universes effectively eliminated the holes in reality, hence the many projects to remove amber going on. Maybe since there were no more vortexes and the fabric of reality was mended, maybe things could only get better from there? One could only hope.

Olivia sat with Lincoln and explained the documents he needed to sign, though most were pretty self-explanatory. The consisted of security and privacy pledges, citizen naturalization applications, and other formal forms. Lincoln picked up his new show-me and wondered for a moment where it was they got a picture of him. They could have just used a picture of his alternate, but instead it was him, glasses and all. They must have gotten it when both universes were working together. It was only when Lincoln yawned again did Olivia realize they had been sitting and discussing for close to two hours. "Come on, I think we both need a break. Let me show you around!" She got up, gesturing him to follow her.

"You know, I've already seen this place..." Lincoln mentioned, though it didn't stop him from getting up and following her out.

Olivia signaled the guard who had begun to follow them away, letting him know he was dismissed and smiled over at Lincoln. "Sure, but this is your official tour of the place as a full-time member," she grinned.

"_If_ I pass the tests," Lincoln reminded her.

"Pshh, you'll do fine! Anyway, come on." Olivia gave him a tour of most of the building, including places Lincoln had not had the opportunity to see, such as the infirmary, gym, rooftop courtyard sitting area and the cafeteria. As they walked, Olivia filled him in on how things were run in that universe's Fringe Division. Olivia mentioned that as he may have noticed, every Fringe Agent had to be able to move and act like a soldier and were even given similar ranks.

"You know, I never really knew what I truly wanted to be growing up. All I was concerned about was the then and there," Lincoln explained. Olivia kept quiet; she knew what he spoke of already as her old partner had mentioned something very similar to her once before. It seemed both Lincolns stayed on a pretty identical course up until a mysterious point. "I pretty much stumbled into Fringe Division when I needed to get answers for... for my own previous partner's death..."

"It just leads to more questions, doesn't it?" Olivia added sadly. They had slowed in their walk, delaying going back to the cells.

"Yes, it does..." Lincoln adjusted his glasses, finding the polished floor by his boots fascinating. "I got answers, but they were more confusing and frustrating as I had hoped," he sighed. "Anyway," he shook himself out of his gloom, "that being the case, I don't think I'd be, ...well, physically suited at all for the job, honestly," he smiled slightly.

"Don't worry, you saw the gym, right? We'll get you in shape in no time!" Olivia put in an extra boost of cheerfulness for him, playfully punching his shoulder. It was not fun if _both _of them were missing their partners and miserable about it. "Hey, what do you say if we stopped by the pub for lunch?"

"Um, well, sure, why not?" How could he say no to spending more time with her? Besides, what else did he have to do?

They went to the bar pretty close to Fringe HQ and aside from different though strangely similar drinks than Lincoln knew of, they had honestly pretty tender wings. Lincoln didn't think that he would like wings, it being really messy and all, but in the end he enjoyed them quite a bit. As they ate, they spoke of differences and similarities in both universe. There might have been differences in that universe, and that world might have been on the mends after being so messed up, there really weren't as many glaringly huge differences. Sure, the twin towers still stood, but aside for architecture and some pop-culture, the people were the same, the customs were the same, the laws were the same... maybe it wouldn't be so difficult to adjust? Even so, as was his way, Lincoln planned to study all he could.

Back at the Division, Olivia and Lincoln were flanked by the armed guards that had been looking after Lincoln in his cell earlier, as though they were leading him back. That was the last straw for Olivia. "Alright, listen up," she stopped them, her firm tone grabbing their attention. "I don't care if it's Secretary Bishop's orders or orders from the President himself, until there is a new chief I am calling the shots here. I am the next in line and you will listen to me or so help me God you will be cleaning toilets for the rest of your career, get me?" Olivia began, pointing at them menacingly.

"Y-Yes ma'am," both of the guards agreed, straightening up just a little. Lincoln stood by impressed. She had all the makings for a commanding leader.

"Good, now, I do not want my partner to be treated like a criminal so unless he asks for escorts around the building, I don't want to see any guards posted around to 'look after' Agent Lee, understood?" She demanded. When they both agreed once more, she nodded and excused them. She had no doubt that the Secretary probably had him followed outdoors, being the paranoid sonofagun he was, but in the building she would have her way. At least, for as long as she could.

Lincoln was touched by the sentiment Olivia displayed and was honored to be called her partner. Still, being horribly embarrassed by the scene made him keep quiet. He hoped one day he would be able to have the kind of self-assurance that so many people there, including Olivia, displayed. After Olivia dropped him off and went off to help Astrid temporarily run the Division, Lincoln sat at his table and looked through the files again. "I better get started. No knowing when I'll be 'evaluated'," he muttered to himself. He only hoped he could retain enough of the knowledge to pass whatever tests they would give him, if it was even relevant.

Back at her desk, Olivia smiled to herself as her phone dialed a familiar number. "_This is Charlie Francis," _the voice on the other end greeted. Odd that he hadn't recognized her ID chime. He must have been busy with bug girl... Ever since that strange case with the bugs - that ended pretty quickly fortunately - Charlie had been getting calls from Mona until he finally called back and agreed to have lunch with her. One thing led to another and they started seeing each other. Olivia always knew bug people had to stick together! Olivia decided she would tease him about that later.

"Hey Charlie! I thought you'd like to know of our new addition to the division..." she trailed off, a little unsure now of this particular subject.

"_Hey 'Livvy,"_ Olivia could hear the smile in his voice. There was a pause. "_Addition? What are you talking about?"_

Olivia cleared her voice, leaned back in her chair and played with some papers idly. She knew she was just delaying telling him now. Maybe this wasn't such a good idea? No, he had to know and would find out eventually... better he find out by her now than by someone else later, right? "Well... remember when both universe were working with us?"

"_Um,_ s_ure..."_

"You know the bridge is closed, right? Someone informed you?" Olivia continued.

"_I was. What's the point you're trying to make, kiddo?" _Charlie asked in concern. Olivia only ever went around in circles when she was trying to stall.

"What if I told you... we permanently had another Lincoln with us now?" Olivia bit her lip, hoping Charlie wouldn't take it badly. Her oldest friend had been incredibly sour that he hadn't been able to make it to Lincoln's funeral. Lincoln had been his friend as well, and his loss wasn't any easier on him. "Charlie?" She prodded softly when he didn't respond.

_"I'm going to have to have you pick me up."_

"What do you mean?" Olivia sat up and frowned in confusion.

_"I mean I left my car there when I went on leave with Mona. I'm taking the first airship back to New York."_

_**TBC...**_

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**End A/N:** I decided to update it again because this beginning part is a little slow, and I had also finished writing this pretty quickly. But don't expect me to update this fast all the time! That being said, I'm sorry if it's a little boring for now. I tend to like to ease into stories before jumping into the action. I promise things will get interesting soon though. Trust me, this story is gunna have lots of tense, nail-biting moments soon!

Shout-Outs:

**Podunk:** I appreciate it! Yes, people tend to overlook the consequences of just jumping into and joining a new universe willy nilly.


	3. Mr Lee

**Days Gone By**

**Disclaimer: **I do not own Fringe, and I do not own the characters, except for Major Gregory Cohen, but I do own this plot for this fan-based story.

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That night, Olivia had left Lincoln with homework, several additional books including military and political ones, not only to keep his mind occupied, but to hopefully help him with the upcoming evaluations. After her shift ended, she bid him a good night, making sure he had enough blankets to create his own mattress, and went home. As she set her things down, back home, and sat on her couch to unwind a bit before bed, she thought of everything that happened so far. The world that she had known had been turned upside down. It was getting a little harder to keep up the overly cheerful attitude these days. First both universes had been at war, then allies... then a man she had trusted so much had brutally betrayed her and their government. Broyles had in a way killed her partner. Walter had said not to judge him, he had after all just been trying to protect his family... but how could she forgive him for all he had done? Among other things for the death of one of her very best friends? Feeling the sting of tears and biting back the anger at herself for getting so emotional again, Olivia decided it would do her no good to think of these things. She glanced at the bottle of brandy still sitting on the coffee table. Shaking her head she got up and went to prepare for bed.

The next morning, Olivia woke up with fortunately no nightmares. She sighed in relief as she got up to prepare for the day. She would pick up her _other_ oldest friend that day. The thought made her smile; she missed Charlie and could use his 'rare' bits of wisdom. His airship would be arriving in two hours from Boston where Mona Foster lived. When she got to the Empire State Building, she went up to the arrivals section and sat down on one of the leather seats provided. The sun had just begun to dance over the city, and she was high up enough in the building to see the golden rays play on the gentle whiffs of steam rising up from the chimneys.

Olivia had never been known for her patience, so she spent the next hour and a half: getting up, walking to the windows, sitting back down, getting back up, wandering the terminal, and repeat. When the announcement was made that the flight from Boston had finally arrived, Olivia all but bounced on her feet in excitement – and relief that she wouldn't have to be 'patient' anymore. She shifted from one foot to the other, watching for Charlie as passengers walked through the gate. When she finally saw him, she waved him over, a big grin on her face. "Charlie, over here!"

"Hey, 'Liv!" Charlie greeted her, setting his luggage down to hug her.

"It's about time, Charlie!" Olivia laughed, hugging him tightly. It wasn't as though they hadn't seen each other in such a long time, but it _was _that they hadn't seen each other since before the funeral. Olivia knew Charlie was still hurting from missing it, even though he open up about it. The fact that he hung on to her, just as tightly, was evidence enough.

"I had no control over how fast the zeppelin moved, 'Liv. What? You wanted me to threaten them or something?" He smiled down at her as he pulled away, giving her a look that told her he was grateful for her not bringing his absence up directly.

"And why not?"

"You've gotta control that impatience, kiddo, it'll get you into trouble one day," Charlie chuckled, letting her lead him out. Once in the car, they sat in silence for a few minutes. Neither of them were quite ready to attempt to speak of what they both knew needed to be spoken of- the reason Charlie was even there to begin with.

"So, want me to take you to your apartment or...?" Olivia trailed off.

"I left my car back at HQ, remember? I should probably stop by there... and, well, I guess meet... Lincoln," Charlie frowned slightly, looking away and out the window.

"Yeah," Olivia muttered in agreement.

They were silent once more, until Charlie couldn't stand the silence and asked what he had been wondering since... _his_ death. "So how are you taking it?" He probed gently.

Olivia smiled sadly. Charlie always went straight to the point when he knew something was bothering her. "Taking what?" Olivia tried the innocent card. It didn't work. It never really could with her, especially not when Charlie was concerned.

"Quit stalling, Livvy, I know seeing him again isn't doing you any good-"

"-Actually-" Olivia interrupted, "-him being here is helping," she recounted quietly. "I'm not sure I can explain it that well, but he's made it easier. It's as though he's _meant_ to be here, I can't explain it," she shook her head, then noticed his expression. "Don't look at me like that." Olivia bristled when Charlie gave her a knowing look. "I mean that he's been here since... his death. He's been here supporting me and- oh Charlie, I didn't mean it that way! I know you couldn't just pop back in and-"

"-No, no you're right," Charlie cut her off. Well there went not bringing it up. He placed his hand on her shoulder and smiled kindly, though fleetingly, at her, letting her know he wasn't upset. "I should have been there for you," he gave her a remorseful look that just broke her heart. "I'm sorry, 'Liv. I should have been there. I might have been able to save him if only I-"

"Stop," Olivia shook her head. "It does us no good thinking of what we _could have _done. We had played it by the book, we thought we had everything covered, 'thought we had our guy..." she sighed and smiled sadly. "Trust me, Charlie, I've been playing the 'what if' card over and over in my head and it just makes me feel sick at the end of the day."

"In that case, why don't we change the subject?" Charlie offered as they got into the car.

"Good idea!" Olivia nodded. Her lips quirked up in amusement and Charlie had an idea what subject she was going for this time. "How are things with you and bug girl?"

"_Mona_ – and they're fine," Charlie answered in a mock-clipped tone.

"You've got to give me more than that! I tried calling you yesterday and it took you way way too long to answer. -And then you didn't even recognize my ringtone!" Olivia added with a grin.

"...She was helping me with something..." Charlie squirmed a little.

"With..?" Olivia probed, glad Charlie allowed her this distraction. She knew it 'bugged' him when she and... 'their' Lincoln, had gone and teased him relentlessly about him dating Mona Foster. The fact that he hadn't told her to drop it, reminded her of just how good a friend she had in Charlie, how he was willing to sacrifice his peace to make her comfort.

"I had... an itch..." Charlie drew out, avoiding looking at her.

It took a few minutes for Olivia to stop laughing before she could speak again. "By 'itch' I hope you mean sex..."

Charlie leaning back against his seat, turning a bit so he could give her his playfully tolerant expression. "You know, it's time like this your snarky laughter makes you sound like a walrus..." he bit back. "And no, I don't mean sex. My um-" he straightened a bit and fiddled with his earpiece, elbow resting on the car door.

"Worms?"

"-_Arachnids_," Charlie gave her another look but went on, "they were," he shrugged, "acting up again..." he finally elaborated.

"Well! At least she's there when they start to _bug_ you, right?" Olivia snickered.

"You're _real_ original, kiddo..." Charlie rolled his eyes, hiding his amusement behind a fake scowl. Thankfully, Olivia mercifully dropped the subject. When she parked in the staff lot, she turned to give him a serious look.

"Remember, this Lincoln doesn't really know you. He knows _of _you but not much else. Like the one we know-... knew, he's been reading pretty much every case file he could get his hands on, but he won't know our jokes or anything. Also... he's a bit of a dork..." Olivia bit her lip, smiling fondly. It wasn't really that she thought that. Lincoln had proven several times that he could hold his own. He had also shown a few times the same shadow of general "badassery" and boldness that his counterpart had proudly displayed like a preening peacock. She knew that the same fortitude, bravado, and commanding attitude was in him somewhere! He just needed a bit of encouragement to help get it out.

"Oh great. 'Gunna have to teach him to be cool all over again..." Charlie faked an eye-roll.

"Yeah right, who taught whom?" Olivia grinned.

"Whatever," Charlie smiled. "At least this Lincoln won't be so damn cocky all the time... right?

"Right," Olivia laughed. Then again, if he were to loosen up and relax a little, gain a little self-assurance... there might be more of that in the future. He and his counterpart _were _the _same person _after all... right? "Just in case though, hide the mirrors," she smiled. As they walked onto the main floor, they spotted Lincoln hunched over his counterpart's old desk, no doubt doing his 'homework'. Charlie was only a little surprised to find that this version of his best buddy was a little more pale, a little slimmer, wore glasses, and a neatly pressed suit... oh who was he kidding! The Lincoln he was familiar with never dressed so formal! _Captain_ Lee had gone for the 'bad boy' image, cocky attitude, and wicked smiles to the ladies to, and Lincoln had told this to him himself, bury his slight feeling of insecurity deep down. Seeing him this... given up, lost if you will, was a blow. Even just going by his appearance alone almost seemed to solidify that this was _not _the Lincoln Charlie knew, as Olivia had told him.

"Hey Lincoln!" Olivia greeted him cheerfully. It would take her a while before she could start calling _him _by his nickname... but she knew she would get comfortable with that soon enough.

Lincoln tore himself away from his research and looked up, already brandishing a smile to her, happy as ever to see her. "Hey, 'Liv," he greeted back. When he noticed Charlie beside her, he stood and walked over to them. "And hello... Charlie?" he guessed, having only read about him and seen his picture once or twice.

"That's right," Charlie nodded and took Lincoln's offered hand. "Nice to meet you." Lincoln could see a sort of wistful look cross the older man's eyes before it vanished. "How're they treating you here?" Charlie queried, sitting at his desk in front of his while Olivia stood next to them.

"Tell you truth, since I decided to stay here, I haven't much had a chance to go out," Lincoln shrugged. "But besides that and the few _security measures _placed on me," he snorted softly, "they've been treating me well I guess."

"Security measures?" Charlie's scarred brow lifted.

"They're following him around and posting guard detail on him," Olivia explained with a sneer of disapproval.

"What'd you do?" Charlie smirked. "You must have gotten someone pissed off or something?"

"No, -well... I mean, I may have illegally crossed over to this side once and helped... kill two agents -who weren't who they said they were by the way- and caused a bit of trouble in general," Lincoln shifted slightly in embarrassment, his gaze returning to his desk.

"Wow, that's it then, you're nothing like your double," Charlie said in mock-surprise. "The Lincoln I knew would never break the rules like that," he grinned.

"Hey, I- he- uh, we? I don't know about the Lincoln you knew, but I wouldn't just break rules for half-assed reasoned either. There happened to be a very solid, good, right reason," Lincoln defended, though at this point he was slightly confused as to who he was defending.

"I know, I'm just messing with you," Charlie chuckled.

Later that day, when no case was presented to them, Olivia suggested they go to the diner for some _tea_, to get better acquainted. Fortunately, Astrid was more than willing to 'hold the fort' while the three went out, knowing they would rush back in if she asked for them. While sitting at the bar, the trio talked about everything and anything, until Lincoln mentioned New York looking strange to him, as if he were looking out into the past. He explained the tragic loss of the twin towers, and the souls that went with it. It was enough to get both of the Fringe Agents he sat with misty-eyed. Changing the subject landed them not surprisingly on differences in their universes. Neither Olivia nor Charlie could imagine that the popular hero Mantis, was in fact a villain in Lincoln's old universe.

"You told me that 'nothing says badass like a flying rat' ...but is a flying insect that much more badass?" Lincoln asked with his own brow lift.

When Lincoln took his glasses off to clean them, Olivia paused, blinking in surprise. Maybe it was the light of the day, the late afternoon shining through the window and dancing over the angles of his face. Maybe it was the normally neatly combed hair, now messy from the wind that day. Maybe it was the look of concentration on his face – his perfectly shaped brows furrowed, darkening those eyes that could burn into you, or the way he wet his lips with the tip of his tongue. At that moment, he looked like a strange blend between both versions of himself. "I suppose not." Olivia's response was less than strong. That tingling feeling she got down her spine was because of the cold, not anything else, damn it.

"I mean, at least batman wore black and stuck to the shadows, relying on fear to intimidate his enemies... Mantis wore green and flew around swatting at people," he went on. It wasn't exactly a smirk, but it was as smug as Olivia had ever seen this Lincoln be. The corner of his lips tilting up slightly. Before she could stop herself, and wonder if Charlie spiked her drink again, she wondered if those lips were as soft and inviting as they looked.

"Hey, don't trash it 'til you see it for yourself, buddy," Charlie chimed in, mercifully jarring Olivia from herdangerousthoughts.

"It just goes to show you that different choices can lead to wildly difference outcomes," Lincoln mentioned. "That reminds me, I've been meaning to ask since you introduced yourself. I knew I saw you from somewhere, but it wasn't _you _who I remembered. I read about your counterpart, who... a shapeshifter killed and impersonated," Lincoln paused, his vision going somewhere else, to a bad place. Olivia saw the pained expression and recognized it. It was the same expression she had when she looked in the mirror these days. Again, before she could think about what she was doing, she reached over and placed her hand on his over the table. It worked to distract him, sure, but it also had an unexpected outcome. Neither of them could have expected the almost static-like charge to spark between them at the simplest touch. Their eyes met, both of them at the same time confused and surprised. Olivia saw him swallow hard and was oddly pleased that it affected him too.

"And?" Charlie asked after the younger man hadn't continued. Charlie hadn't missed the interaction between the two, nor had he missed the look they gave each other. Oh he was going to have fun watching those two. Strange that Olivia hadn't reacted that way with the other Lincoln, but perhaps it took losing him to open her eyes, as sad as that was. Maybe she would have another chance though? That is, if either of them acted on it.

Lincoln blinked back up at him and took a few minutes to gather his thoughts before answering. "I read on his file that during a mission to apprehend a man conducting experiments with different animals"- to this Charlie rolled his eyes and Olivia grinned, "-he was attacked by a mutated creature. This is probably personal, feel free to not answer but... do you have-"

"They're _not_ worms," Charlie sighed, having recognized the case immediately. Of course, this sent Olivia into a fit of laughter, surprised but delighted by the turn of events.

"I swear I didn't put him up to it!" Olivia waved her hands in defense at Charlie's pointed look.

"I don't understand," Lincoln frowned in confusion, leaning back in his seat. His glasses slip down the bridge of his nose a little. He pushed them up with one finger as he leaned back in, a look of question in his eyes. Olivia caught the look and recognized it, a pang of sadness, and at the same time wonder, fluttered through her.

"It was a running gag between Olivia and the other Lincoln," Charlie explained. "I have... spiders dormant in my veins," he saw the grimace Lincoln gave him, followed by the look of sympathy. "Yeah, it's not fun. Anyway, those two-" he gestured to Olivia, "-knuckleheads would tease me about having worms like a dog or something," he shrugged.

"Aw, come on, you loved it," Olivia brushed the tears of mirth from her eyes and grinned. Perhaps they weren't just from mirth, but the boys didn't need to know that.

"Is that when you got your scar?" Lincoln queried after Charlie explained the situation he had gotten himself into. He took a sip from his now cold tea and he blanched in disgust, setting the cup back down. His heart beat just a little faster when his fingers brushed against the redhead in front of him.

"No, but that's a story for another time, I think. Shouldn't we be heading back? I have some stuff I want to do before my flight back," Charlie said, pulling out his wallet to tip the waitress before Olivia could.

"You're not staying?" Olivia asked sadly.

"No can do, kiddo. I gotta get some stuff taken care of first." Charlie's answer was mysterious, a little smile playing on his lips, knowing Olivia would be impatient for an explanation as usual. Fortunately, she hadn't probed him for more information.

Oh Olivia knew she could have gotten more from Charlie, but she had a feeling she knew what it was he was hiding. She hadn't missed the soft smiles when he spoke over his phone to Mona Foster, or how many times he checked his watch. Those two were a lot closer than Charlie admitted out loud. ...But that wasn't exactly the only reason either. Glancing up at Lincoln as he and Charlie spoke a bit more while they walked out of the diner, she couldn't help remember how strange that bit of contact between them had been. She had never really seen Lincoln as more than a great friend and trusted ally... sure she had maybe a little crush on him once, before he opened his mouth, but it hadn't ever been more than that. They had never crossed that line. Then again, would they have it Frank hadn't been in the picture? She just wasn't sure.

But now... this was... it was different somehow. This Lincoln hadn't had the background that she and his counterpart had. He was in a sense a completely different person. All Olivia really knew was that it was a new and surprisingly pleasant feeling. What did that say about her? About her loyalty? About the kind of person she was to be attracted to one side of the same man? She hoped that neither of the men had noticed her silence.

Back at the Division, they separated to complete their own tasks. This gave Olivia enough time to think about what had happened. If she was being honest with herself, she would admit that this strange sort of tension between them had been around the very moment they met at the pier with Peter Bishop. Standing between both versions of him had been almost surreal. Back then she had noticed only the stark differences between them, but the more she had begun to work with _this _Lincoln, the more she realized how much they were alike, and how much 'her' Lincoln had seemed to keep hidden. Again, it always came down to the fact that they were essentially the same, didn't it? But the thing that confused her, was that even though she knew they were the same... they were also different at the same time.

This Lincoln seemed a lot more open, in a sense, not quite as guarded as her partner had been. While his counterpart acted like a hotshot soldier, calling the shots and walking with a strut, he hid his inner feelings behind a mask of indifference or joviality, more times than she could count. But _this_ Lincoln? You could read his emotions on his face as clearly as a picture. Seeing him like this, instead of so guarded and evasive, was surprisingly pleasing to her. So yes, she could admit to herself that she was growing to _like_ him, a bit more than she probably should maybe. And once more, this served to fluster and confuse her at the same time, not that she'd project that if she could help it.

Brushing the unproductive thoughts from her mind, Olivia went back to her paperwork. It was too bad she couldn't have predicted Lincoln would decide to sit behind her in his counterpart's seat to continue studying. She smiled over at him when he sat down and tried to get back to work. Her own inner admissions played in her head and she scoffed inwardly in annoyance. By the end of the day, Olivia was so wound up she visibly jumped when Charlie placed a hand on her shoulder, no doubt trying to get her attention. "'Liv, I asked if you wanted to see me off?" He asked gently.

"Yes, of course," Olivia answered, getting up maybe a little too hastily. Since Charlie took his own car this time, Olivia and Lincoln rode together in silence. By the time they got to the Empire State Building, there was a tension thick enough to cut through between them. Olivia knew that Charlie noticed, but was thankful that he didn't bring it up.

Charlie put his hand out to Lincoln, who smiled and shook the offered hand. "You take care of our Olivia, okay?" His voice was gruff with emotion.

It was obvious to Lincoln who Charlie was thinking of when he said 'our' though he couldn't be exactly sure. It didn't matter, of course, since Lincoln would try to take care of her even without the reminder. "O-Of course," Lincoln stumbled over his own words, wincing slightly at how awkward that sounded. Oh how he wish he had his alternate's self-confidence!

Charlie chuckled and gave him a friendly pat on the back. "And you-" he pointed to Olivia, "-get this geek to loosen up a bit!" The pat on the back became a small shove, making Lincoln stumble toward Olivia.

Olivia caught Lincoln before he stumbled all over her and helped steady him. She shook her head in disbelief and grinned at her old partner. "Oh don't worry, I have loads of plans for that in mind."

"Just keep it PG," Charlie smirked.

"Hey... I'm right here you know..." Lincoln couldn't stop the blush of embarrassment this time. Just what had he gotten himself into? Just then the arrival of Charlie's flight was announced.

Olivia watched the new friends bid each other goodbye with a fond smile before taking her turn and hugging Charlie. "You better come back soon, okay?"

"I'll be back before you know it. Take care of each other," he smiled knowingly. Olivia rolled her eyes and punched his shoulder in a familiar playful manner. When Charlie had gone, the ride back to HQ was a lot lighter for the two friends. They spoke of how good a guy Charlie was, and how Lincoln could see why they made a good team. By the end of the evening, things seemed to have gone back to 'normal' between them. Or so they hoped. Olivia bid her partner goodnight once more, asking if he needed anything but as before Lincoln declined. She had wanted to ask if he'd like the spare room in her apartment again, but she couldn't bring herself to ask again... she didn't know what exactly she would really be asking him. And that thought scared her. As Olivia lay in bed that night, she wondered not for the first time why it was that she suddenly felt so different around this Lincoln.

The next morning, just as Olivia greeted her new partner, Astrid went over to them and announced that the new chief was in Colonel Broyles' old office and wanting to meet them. As they walked, Olivia noted that either Lincoln lost his razor, or he had been having a hard time sleeping himself. The hint of stubble over his cheeks was a surprisingly welcoming sight. She always thought he looked better with a bit of fuzz, though she had been damned to tell him. She wondered how her new partner would react to the compliment. Would he puff out like his counterpart? Or smile and look away in embarrassment? Would he do a combination of both?

The doors swing open and Olivia noticed that she must have stopped walking. Lincoln's hand was on her elbow, gently trying to nudge her forward. "Sorry," Olivia felt herself blush and rolled her eyes inwardly in irritation. She couldn't understand what was with her those days.

Their new chief, Greg Cohen, was a stout man with neatly trimmed black hair, graying on the temples, and hard lines on his face. His eyes were hard as he studied them, but if Olivia looked hard enough, she could see laughter lines on the edges, creasing his eyes in an almost welcoming way. "Good morning, agents. I am Major Gregory Cohen" he introduced himself. He sat at, what was now _his _desk, and looked over the files sitting atop it. "I've heard good things about you, Agent Dunham, and you too, Agent Lee," he said, glancing over at the younger man.

"Sir, I'm not..." Lincoln was unsure of how to broach the subject.

"I am fully aware of who you are and who you are not, Agent Lee. I was debriefed about the universe you hale from, no need to worry." Greg's hands peaked at the tips as he rested them on the desk. "I hope you're ready for your evaluations, son. Today is the day you prove to us that you have what it takes to be one of the elite."

Olivia glanced over at her partner and saw his jaw tighten, lips forming a thin line. "Yes sir," Lincoln enunciated the words. He knew this day was coming, he just hadn't realized how quickly it would arrive.

"Good man," Greg nodded in approval. "That's the kind of attitude I like to see." He spoke briefly to them about himself, what kind of man he was- the kind that apparently was by the books and sought out answered as efficiently as he could- and what he expected to see from them. After introductions were over, Greg excused Olivia, letting her get to her paperwork that he knew she was slacking on, and explained to Lincoln that he would be tested physically, intellectually, and on general but much needed information. When his debriefing was over, Lincoln began his long day of evaluations.

No one could argue that Lincoln Lee was intellectual. He was about the sharpest tool the psychiatrist, Anne Rivers, had ever seen. What was interesting to note was how much alike in answers he and his alternate had had. They were both exceptionally bright men, which could account to why Captain Lee had been promoted so quickly and this Lee had been such an interest to the Secretary of Defense himself. Despite his prowess at this field, however, his lack of understanding of how their Fringe Division worked, though similar to his own, and lack of knowledge of some key bits of history and information, was a damper in his results. Dr. Rivers just hoped that Agent Lee would pass these tests the next time he was evaluated. Like his counterpart, she hoped he would go far as well.

By the time Lincoln's last test was finished, the physical trial, obstacle course, marathon, what have you, he was sure he was done for. He had liked to think of himself as in shape before, he could catch a bad guy when he needed to, could drop down from quite a bit of a distance and land on his feet, but apparently this universe's Fringe Division required their agents to be more soldier than Lincoln had thought. It wasn't just a rank. Lincoln thought idly as he braced his hands over his knees in fatigue, that maybe it would do him some good to enter the academy attached to the Division... or at least get someone to help him out. After a painful though at the same time soothing hot shower, Lincoln stood clean and proper in front of the man looking over his test results.

Greg's frown seemed permanently etched in his face. "This is disappointing," he sighed. "I had high hopes for you, Mr. Lee," he added. Lincoln didn't miss what Greg had called him and stiffened at the implications. Greg's face softened a bit as he set the tablet down. "I'm sorry, son, but you're going to have to do a lot better to get back on the force."

"I understand," Lincoln responded evenly. His gaze was fixed on a point straight ahead of him. Jaw firm and posture straight.

"Look, I know this is hard on you, son, so I'll tell you what. We have a company hotel, if you will, walking distance from the building. I will make arrangements for you to stay there, in much more comfortable living conditions, so you can focus better on your training. I still want to see you succeed, my boy, so don't give up just yet, alright?" Greg hadn't finished speaking before he pulled out the proper documents he needed to make the arrangements over his desk computer.

Lincoln felt himself relax slightly. He was very grateful to this man, this man who didn't even know him, who was willing to do so much for him already. "Thank you, sir."

"Not a problem," Greg waved his hand in dismissal. "Go collect your things, you'll have a room booked soon enough."

Lincoln nodded and did his best not to fall over as he exited the office. Whether it was out of exhaust from the mental and physical exercises he had gone through that day, relief that he wasn't going to be dumped out in the rain – so to speak, or a combination of both, he wasn't sure. All he knew right now, the only thing he cared about, was that there was only one person he wanted to speak to at that moment. Unfortunately, as she wasn't at her desk, he had no idea where she was. "Hey, Astrid?" Lincoln greeted the dark-skinned agent in a friendly manner. Astrid blinked up at him, and Lincoln wasn't sure, but he could have sworn he saw a fleeting smile pass her so quickly he might have imagined it. It made him wonder how starved Astrid was for familiarity.

"What can I do for you, Agent Lee?" Astrid asked, a slight tilt of the head being the only clue that she was curious.

"Do you know where Olivia is?"

"Yes. She has gone to the diner near headquarters and asked me to ask you if you could join her when you were finished with your tests. How did they go?" Astrid's faster than light response, followed by an abrupt question made Lincoln mentally trip for a moment before he remembered she had asked him a question.

"I didn't meet the requirements... but Major Cohen is allowing me to stay at the nearby hotel and prepare to take them again at some other time," he answered.

"That is good," Astrid nodded.

"...Yeah. Thanks Astrid, I'll see you around," Lincoln nodded to her and went to his cell. He found an empty box sitting by the door and figured the Major had gotten someone to get it for him. Lincoln looked around the cell and figured that with as few a things he had, he probably didn't need a box of that size. Even so, he gathered what little he had been given or had acquired and piled it into the box. Stepped out, he breathed a sigh of relief to finally be leaving his prison-but not prison, and walked out to the now familiar path leading to the diner.

"Lincoln," Olivia greeted him where she sat at the bar. Lincoln smiled tiredly at her and set the box down on the floor, and then promptly slumped onto the stool next to her's. Olivia saw the weary and disheartened look on his face, recognizing it as being the same look of disappointment she had seen on her previous partner's face, and frowned in concern. "Not good?" she asked softly, knowing the answer.

"Call me Mr. Lee, from now on," Lincoln said, his tone a step away from being brooding.

"I'm sorry, Lincoln," Olivia said sympathetically. "Failed the 'intellectual' test, did you?" she tried teasing him.

"That was the only one I passed," he scoffed. Olivia knew he wasn't angry at her, but it didn't stop her from being surprised at how cynical his attitude suddenly was. It was then Olivia really took note of the box.

"They kicked you out?!" She asked in outrage, resisting the urge to shoot up and march over to Greg Cohen to give him a piece of her mind.

"No, Cohen got me a room at the hotel nearby and encouraged me to keep training." This was the first time since he arrived that Olivia could see a hint of a more positive expression.

"That's a relief," Olivia sighed inwardly and forced herself to relax. "So what's the problem then?"

"I don't think I'll be able to train hard enough to meet the requirements for _this _Fringe Division. I had no idea they needed you to be as fit as an actual honest to God soldier," he explained. "I've never thought of myself as an athlete, though I thought I was in pretty good shape," he shrugged. "The knowledge of your universe I can get down easy, but the physical training I don't know." In truth, Lincoln was fairly certain if his double could be as fit as he needed to be, so could he. But honestly he just wanted Olivia to offer to help him. It was not selfish _at all_.

"I could help you with that, if you want..." Olivia offered and Lincoln felt himself shout for joy inwardly.

"Well, I guess if you insist..." Lincoln's lips twisted up into a tired smile, yet somehow it was slow and easy at the same time. It was both familiar and at once new to Olivia. The gentle crinkle in his eyes, telling her that he knew something she didn't- which for some reason didn't bother her at the moment- followed by how unguarded he was at that instance... was that her breath coming up short? Or was it his from the long and tiring day? She convinced herself that the quickening beat of her heart was just her imagination.

"I do," she smiled back, refusing to show the bizarre weakness she was feeling around him lately. That didn't stop her from shivering slightly when his eyes on her seemed to suddenly tense. The dorky, yet oddly charming glasses did nothing to filter his penetrating gaze this time. Lincoln, the other one, had only looked at her like this once more, when he had kissed her that one time, long ago.

"_I do," Olivia smiled warmly, gazing lovingly into his eyes, her own slightly wet with emotion. Lincoln felt himself fill with joy, not able to believe this day had finally arrived._

"Earth to Lincoln?" Lincoln blinked back to reality and blushed, forcing the embarrassing fantasy from his thoughts. "I asked if you're really okay with it?" Olivia repeated, her voice not quite as strong as she'd like it to be.

"Err, yeah, sorry, of course I am," he smiled nervously, not for the first time wishing he had the same confidence his double had had. "I'm going to need all the help I can get," he told her. He just hoped he knew what he was getting himself into. That much proximity to her might actually fry his brain.

And perhaps, her's as well.

_**TBC...**_

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**End A/N: **Another boring chapter here, I'm sorry! The reason it is so incredibly long is because to sort of skip over the boring stuff, I decided to combine two chapters. Don't expect many chapters to be this long! I promise the next chapter will be fun, I have some very interesting things planned... I hope everyone enjoyed seeing Charlie again! You can expect to see more of him!


	4. Biohazard

**Days Gone By**

**Disclaimer: **I do not own Fringe, and I do not own the characters, but I do own this plot for this fan-based story.

* * *

The already severe lines on Major Gregory Cohen's face hardened as he listened to the information Astrid Farnsworth gave him. When she was finished, he sat back with an audible breath, weary and just a little angry. "How long has it been this way?" His words were clipped and formal, though that wasn't so strange for him. Greg Cohen prided himself for being cool, collected, and presentable. But this case...

"Approximately twenty-three hours and eight minutes," Astrid responded, cutting his dour thoughts off. "There have been eight confirmed deaths so far, but at the rate it is advancing through the facility there could be many more very soon." One could never really tell all that well what emotions Astrid was trying to convey, but you knew it was serious when she started to talk a mile a second.

Greg rubbed his face with his hand, already exhausted and the day hadn't even properly begun yet. How had they been oblivious to this until now? Why had they _just _reported this? Were those experiments they were conducting so secretive that they had to wait until the last, worst possible minute? "Alright," Greg nodded grimly and looked again at the list he made of recommended agents for this mission. "It's a shame I only have one agent here qualified for this type of mission. Captain Lee or even, as I recall reading about him, Agent Francis would have been an asset to this mission."

"Sir, if I may?" Greg looked up to the camouflage clad young woman. "_Agent _Lee is just as qualified as them and has been a very substantial help to us in previous cases."

"Let me be the judge of who's qualified to do what, Agent Farnsworth," Greg reprimanded, though in not at all a severe tone. "At any rate, Olivia Dunham certainly _is_ qualified for this case and is still here, so bring her in." Greg sat down as the petite agent left to carry out his request, and perused the records. Charlie Francis was a go-to agent, but he was on leave for another week or so. Oh sure, he could call him in, but maybe Agent Farnsworth had a point? Use what you had? It was only two minutes later when Agent Dunham all but strolled in like she owned the place.

"You wanted to see me, boss?"

"I did. Agent we have a very delicate situation on our hands. At 07:40 yesterday, we began to receive reports from a top secret research facility in Utah that people have started to disappear. We can find no traces of them, in their homes, favorite spots to stop after work, or what have you. They simply vanished. Their cars are still in the parking lot of the facility and we looked into the camera feeds from our drones, but saw nothing of use. It is our hope that they are still in the facility, so we have to try to find them. Understand, agent, that this facility is of great importance to the Secretary of Defense and has given me clearance to select the agents I thought fit for the mission." Greg sat back and waited for her to process what he had just told her.

"Am I to go alone, sir?" Olivia asked, taking the folder her superior handed her. The label "top secret" did nothing to calm her nerves. Just what the heck did this mission entail?

"Would that be a problem?" Greg questioned enigmatically.

Olivia bristled slightly but kept her relaxed stance, feet slightly apart, hands behind her back. "I can handle myself, sir, but I would much rather have backup in a case like this."

"No doubt you realize that qualified agents for this mission are scarce..." Greg went on, leaning forward in his seat to rest his elbows, intertwining his fingers. "Why would you suggest? Mr. Lee needs to get reevaluated, Agent Farnsworth is needed here, Agent Sheppard is tending to his pregnant wife, Agent Harris is out of the country, and Agent Francis is currently out of state on leave."

Maybe Olivia didn't spend a lot of time with other agents, but she couldn't recall meeting the half the people the major mentioned. "I understand that, sir, but there is one agent that could help a lot. _Agent_ Lee-" Olivia didn't miss the brow raise from her commanding officer but soldiered on, "-has had the training for this type of mission, despite what the tests say of him, he is about the best choice you could make right now," she told him.

"Making decisions for me, Dunham?" Greg questioned, though he didn't sound all that upset.

Olivia stiffened slightly. "No sir, I'm just trying to convince you that-"

"No need to convince me, Agent Dunham, I already sent a shuttle over to the hotel. Sit tight while I give him a ring," the major smirked at her stunned expression as he made contact with the hotel. Lincoln didn't have his own earcuff yet, so contacting the hotel was about the best way to reach him at the moment. It didn't take a whole lot of convincing to get Lincoln to take the shuttle over. It only took a few minutes for Lincoln to shuffle into the office. Olivia's brow rose at what he was wearing. Clearly he hadn't had the chance to groom himself for the day just yet. His hair was wet, no doubt having quickly washed it before leaving, he wore only his undershirt and a jacket on top – reminiscent of how her old partner used to dress – and he clearly hadn't had the occasion to shave yet that morning. If it weren't for the glasses...

Greg cut off Olivia's increasingly confused thoughts and began to fill Lincoln in on the mission. "So you're telling me we have a 'Resident Evil' case on our hands?"

"I'm sorry, what?" Greg gave him a confused look.

"Resident... nevermind," Lincoln sighed inwardly, but didn't miss the look of amusement Olivia threw him. Olivia didn't quite know what he was talking about, but had a pretty good idea. She thought he might be talking about his universe's version of Biohazard, in which case she had to agree.

"In any case, Secretary Bishop has a personal interest in this mission, that being said, I will need his approval for your involvement in this, Agent Lee," Greg explained. It took him a few minutes going through channels until Greg was able to reach the Secretary of Defense. Once he did, however, he put the call up on the newest addition to the room, a large view screen. Bishop greeted them formally, as he always did, and the went on to explain his personal investment in the research lab, as it was one of the labs responsible for creating some of the tech they used to defend their world... including from vortexes. Bishop may have developed amber in his lab, but it was in that research facility that he had perfected it and implemented it into the canister release devices. "And Lee's involvement in the mission, sir?" Greg asked at last.

Bishop glanced at the major before fixing his gaze on the younger man. "I know what Agent Lee is capable of, major. He has demonstrated himself to be a capable agent on several occasions. He has my support for this," Bishop answered. "Listen to me well, son," he addressed Lincoln, "if you do well on this mission, there may be some exceptions for you in your continued career here, understand?"

Lincoln felt a well of joy fill him, making it hard to stay still, but kept his outward appearance as collected as he could. "Yes sir, I understand. Thank you, sir." Bishop said nothing more, but gave the barest hint of a smile and a nod in response. Olivia, on the other hand, grinned with abandon and bumped her shoulder against Lincolns, happy for him.

"Good, then from now on and until further notice, your new title will be consultant. Do well and you'll go far, Agent Lee," Bishop added and then turned to Greg. "I have ordered my private jet to be fueled for this mission. The security of this lab is of utmost importance. I expect things to be taken care of quickly and silently," he finished.

"Yes sir," Greg nodded. When the signal was cut, Greg turned back to his agents and sent them off to prepare for the mission, letting them know a small team of agents were already there awaiting their lead.

As they drove to the airport, Olivia practically bounced with excitement. "What's with you?" Lincoln asked in bemused amusement.

"I've never ridden in a real jet before! I can't wait," she smiled, her face practically lighting up.

Lincoln's eyes softened a fraction. "Really? It's pretty common where I'm from," he mused in surprise.

"The common source of transportation _here_ is either car or zeppelin. Trains are still used too of course, but airships tend to cover distance better," the red-headed agent explained cheerfully.

The jet was your typical sleek and white small aircraft. It was slightly different looking than Lincoln was used to, and if he wasn't mistaken, remotely controlled. Olivia might have been excited, but suddenly he felt queasy. Aboard the plane, Olivia watched her partner slip on his new earcuff he had gotten from Greg before leaving and smiled. He really was looking more and more like _him _every day. Olivia wasn't sure to feel at peace or torn. She settled for not thinking about it at all, especially since the plane had powered up and was rolling down the runway. Olivia was not so distracted with excitement to not notice Lincoln's sudden bout of nerves. She saw him clutching the arms of his seat rather tightly. "You okay there?"

"Hm? Oh, yeah, I uh, I'm not used to automatic planes," he smiled nervously. "I hope there's an in-flight movie at least..." he tried to joke. The flight to the research lab was maybe a little faster than it would have been back in Lincolns "old" universe, but it still took a few hours. By the time they got there, it was already well into the afternoon. By that time at least Lincoln had calmed down enough to talk and yes, even joke a little bit with his partner.

"So then he throws up all over the guy next to him!" Olivia laughed. This was a story about Charlie she always loved to tell, even to Charlie himself who would simply roll his eyes and deny the incident.

"What'd the guy do?" Lincoln asked, an amused smile playing on his lips.

"He tried to beat him up, of course! Real big guy, arms like logs. Charlie tries to be diplomatic of course, saying 'sir, please calm down, it's a perfectly natural reaction'," Olivia said, lowering her voice to copy Charlie's tone, laughing as she did. "But the guy just gets _red_ with anger..."

"Let me guess, you stopped him? Broke his hand or something before he could land a punch?" Lincoln smirked.

"Something like that," Olivia grinned back. Olivia hadn't missed the very familiar smirk her partner had given her just then. For the first time in weeks though, it simply brought a smile to her face. Maybe she was finally getting over it? "I mean, all Charlie had to do was flash his badge and things would be peachy. I had to get in front of them and do it myself," Olivia rolled her eyes. "The guy wasn't convinced though, or maybe just too stupid angry, but he went to punch Charlie anyway. So naturally I had to knee him in the gut and take him down, arrest him for trying to assault an officer," she grinned.

"Naturally," Lincoln chuckled softly.

"Charlie will try to tell you that he was the one who beat the guy up of course," Olivia rolled her eyes, a fond smile playing on her lips.

Once they landed, the fun and games were over and the nerves over the mission returned. They didn't waste time exiting the plane. "Here," Olivia handed him what looked like an energy bar. "No time to stop for a bite to eat unfortunately," she added. They finished the last touches of adjusting their gear and boarded the SUV awaiting them there with the rest of their team. It was clear the other agents had had their fair of missions such as this before, if their silence and, frankly, bored expressions were any clue. Then again, it could be that they were not as informed as she and Lincoln were about the mission.

The ride to the lab was mostly silent, and if it wasn't for the fact that Lincoln's thigh was pressed right against Olivia's, she might have tried to lighten the mood. As it was, she was distracted and slightly confused by it. Since when did she become flustered around Lincoln? ...Not that she was flustered, of course.

When the finally reached the lab, an hour of silent driving later, they began to notice things off about it already. There was no movement, whatsoever, the windows were dark, and there were no guards there to greet them. Driving into the parking lot, the six agents quickly took positions, upholstering their weapons and moving silently and purposefully to the main entrance. It was an eye-scan entry system to what looked like an airlock – no doubt to keep any pathogens they experimented on inside. Olivia stepped forward, having been given access to the building from Bishop as the team's leader. The door slid open with a loud hiss.

The sickly sweet, rancid smell of death was the first thing to immediately hit them.

_**TBC...**_

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**End A/N: **Didn't I tell you things would start getting exciting soon? Please let me know your thoughts on this story so far!


	5. Infestation

**Days Gone By**

**Disclaimer: **I do not own Fringe, and I do not own the characters, but I do own this plot for this fan-based story.

Warning: Language and gruesome images ahead!

* * *

Walking through the airlock, the agents stepped into a dimly lit hall. Marks on the wall, including bullet holes and what looked like dried blood told them all they needed to know. Something went wrong here. Horribly, terribly wrong. Smears on the floors led frantic paths, echoes of struggles long dead. Creeping down the halls silently, the six nervous agents were acutely aware of every noise around them, from the hum of machinery in the distant background, to the squeaks of their boots on the once polished floor. The halls were silent besides that, though hisses could be heard behind the walls.

Were those the sounds of monsters in the shadows?

It was too dark to navigate properly, not even the blinking, sweeping red light of emergency power was enough. In fact, it only seemed to worsen the situation. "Switch to NV," Olivia whispered. The group pulled their goggles from their vests and slipped them on. As they neared a room, the door open just a crack, they tensed. Closer the crept, breaths held and muscles tense. Suddenly, a loud hiss erupted from the adjacent hall. They six jerked their guns toward the sound, fingers poised over the triggers of their weapons.

Nothing.

Steam escaped a series of pipes and the team relaxed a fraction. Taking point, Lincoln slid across the wall, poking his head, and the night vision goggles into the room. It was empty. Taking a relaxing breath, he went in, sweeping the area for clues. No bodies, no blood. But there was a strange brown substance on the floor. "Maybe someone was scared shitless?" Lincoln jumped in surprise, not having heard Olivia follow him in. If it weren't for his training, he might have fired a shot from his pistol on reflex. "Sorry," Olivia smiled apologetically, patting his shoulder.

Olivia's hand lingered on his shoulder a moment too long, perhaps. Not that Lincoln was counting how long it was or anything. "I don't think that's excrement," he answered distractedly, leaning in for a closer look and ignoring the feeling of loss when she pulled her hand away.

"Wait, what was that?" One of the other agents asked. In the distance there seemed to be a muffled groans.

"Maybe it's one of the scientists?" Olivia ventured.

"Let's hope so..." another agent muttered.

"Come on," Olivia took point this time, leading them through the hall. More doors lay before them, most of them closed. There were windows in some of the offices, but it was too dark in the rooms to see much. Blood covered one of them, they decided to investigate that one last. Moving closer, they heard what sounded like breathing. They crept upon a windowless door, hearing a soft scraping noise from behind it. Nodding to the team, Olivia silently instructed them into a covering position. Lincoln, with his quick and light weapon, took his position in the front, ready to fire upon any conceivable threat behind the door.

They relaxed slightly when nothing was behind the door and moved stealthily inside. Aside from a wall of monitors – obviously a security room – and another door on the other end of the room, there was nothing much of interest. "See if there's anything useful to see," Olivia told one of the agents as she pulled her goggles up. The room was fairly well lit and the night vision was not needed at the moment. The agent nodded and sat down at the monitors.

As they continued their search, they approached the other door. A soft scratch made the six of them pause and stare at the door. Lincoln raised his pistol once more and nodded, letting them know he was ready. Another agent carefully opened the door slowly while the others prepared for whatever came next.

The attack was sudden, though not completely unexpected as the evidence around them suggested. Lincoln fired, but the assailant was so quick that the bullet only grazed its face. "What it God's name-!" one of the agents began to yell, but his words were turned into screams when another attack from behind caught them off guard. "Get it off! Get it off!" the agent fired his rifle, trying to reach behind himself with it where whatever it was that grabbed him was. One of the other agents rushed over and pried the grotesque looking thing off of him, but was unable to get away from being attacked himself.

"Shit!" The man screamed as the thing, in rage it seemed, tried to claw and bite at him, tearing through his Kevlar. As soon as the first attacker was dealt with, the others tried to help them as well. They were unable to do much however, before the thing attacking them released something from its mouth, spraying into the air. It was only because the agent tripped and fell backwards was he saved from the spray. A second later, Lincoln fired the clear shot he had been hoping to get, hitting the thing square in the head. The 'creature' fell with a heavy thud. "What the fuck is going on?!" The agent demanded.

"That's enough!" Olivia hissed and bent down next to the unconscious man. The 'creature' wasn't a thing or an animal at all.

"It's... a man?" Lincoln frowned in confusion and knelt beside her. The man was once a security guard, if the uniform and empty holster hanging off his belt were any clue. His face and hands were the only visibly exposed flesh and were heavily mutated. Growths which looked like cancerous tumors were abundant, as well as cracked nails, blood-shot eyes, and what looked like a rapid loss of hair.

There was that same brown stuff over the guard's mangled face. It didn't look like dirt, but it did look like what he had exhaled earlier. Something in his lungs? "What do you make of it?" Olivia leaned in for a closer look, but Lincoln grabbed her by the shoulder, gently pulling her back. Just then more of the dust seemed to shoot out, though the scientists was still quite dead. "Yikes, thanks."

Lincoln leaned back and frowned in concentration, scratching the shadow on his jaw idly. "It looks like it could be spores of some kind. We might be dealing with fungus, but I could be wrong," he explained. He shuddered slightly but kept his bad memories to himself.

"Now that you mention it, it did look like he was releasing spores," she agreed. She would ask him about his little noticeable effect to the situation later. Stepping back, she attempted to make contact with Major Cohen, nodding to Lincoln and linking him to the call as well. "Sir," she began when she was connected with him. She explained how they were attacked by a man grotesquely deformed by what looked like fungus, and what appeared to be a release of spores, no doubt to infect others.

"I suggest we quarantine, just to be safe, sir," Lincoln added.

There was a long pause and the team could almost hear their superior thinking. _"Very well. I will send the CFDC. Understand that discovering the root of the problem and solving it is your main objective. Everything else is secondary." _Greg reminded them. _"I will inform Secretary Bishop. Keep me informed of your progress."_

"CFDC?" Lincoln questioned after the call was disconnected.

"Center For Disease Control? Don't you have that in your old universe?" Olivia threw back with an incredulous look in her eyes.

Lincoln responded with an exasperation expression. "Yes, of course, but we don't put the 'F' in 'for' in the abbreviation," he explained.

"Agent Lee? Agent Dunham? You better come take a look at this..." the agent hacking into the monitor system said. Lincoln and Olivia walked over and peered into the monitor.

"People?" Lincoln blinked.

"Survivors. Witnesses," Olivia agreed. "We need to secure them and try to get information from them about what the hell is going on here," she added.

"Agreed," Lincoln nodded and turned to the other agents. "Well you heard the lady, let's go," he gestured them to get ready. Slipping their goggles back on, the six spilled out quickly and quietly into the halls once more. As they moved through the corridors, they could hear sobbing, almost too quite to hear clearly. Once they reached the door where the noises came from, Lincoln steeled himself and once again positioned himself in front of the door, finger hovering near the trigger. The door opened and Lincoln's eyes swept through the room. No attacker, no immediate danger.

When Lincoln saw the group of scientists crouched and crowded in one corner, fear written all over their faces, he relaxed, taking his finger away from the trigger. Motioning the others to follow, the six moved into the room as quickly as they could. One of the agents shut the door silently behind them as Lincoln searched for a light. Once he found it, he told the others, allowing them – and himself – to remove the goggles before being blinded. The group of frightened people whimpered softly from the sudden light but otherwise made no attempt to move, no attempt to speak.

"Don't worry, we're Fringe agents. We're here to help," Olivia told them. Still, none of them spoke. "What happened here?" she asked, leaning down so she was eye-level to the huddled group.

The scientists were silent for a moment, before one of them swallowed her fear and spoke in a weak voice. "We-we were attacked... there was, something went wrong... one of the experiments," she shook her head and buried it in her folded arms.

"What is it? What experiment?" Lincoln asked from where he stood nearby.

The scientist took a breath to calm herself. Even her breathing seemed to tremble. "It was... -oh God, Julian... he told me he-he inhaled some of the spores... we should have known... we didn't mean to... he was the first," the young scientist shivered.

She was losing her patience a little, but Olivia knew if she rushed her, she would lock up again. "I don't understand, please explain," Olivia encouraged as gently as she could manage.

"At first he seemed fine, for the first five minutes or so at least... and then he just collapsed. We took him to the infirmary, I suppose no one mentioned the spores, we hadn't even thought of that affecting him like that!"

"He turned into a monster!" One of the other scientists added.

"What ...spores? What _experiment?"_ Lincoln pressured. The mention of spores made him flinch slightly once more, making Olivia wonder what was wrong, but he sucked it up and drove on. He knelt next to her and gave them a leveled look. "We're trying to help but we need more information," he explained.

Just as the other scientist began to open his mouth to explain, a loud thud, followed by foot steps and low groans were heard. "They're back! They're coming!" The team slipped out of the room and shut the door behind them, hoping the survivors would stay safe. As they prepared themselves, they heard what appeared to be a small mob of people rounding the corner.

And then it happened.

Chaos, utter mayhem exploded as the large mob of infected screamed in rage and ran toward them. "Shoot them!" Olivia yelled, squeezing her trigger. Shots were fired in a blaze, lighting the dark hallway with burst of brilliance from the guns. The mob was upon them, some dead, falling over them.

One of them fell on top of Lincoln, knocking his gun out of his hand. "No!" he yelled, rolling away from another attack and frantically trying to find his weapon. He spotted it, under one of the groves that made up the 'modern' hallway. Lincoln got to his feet again and tried to get at it, but was stopped.

"Look out!" One of the agents yelled, pushing Lincoln out of the way as three more infected scientists, stumbled around the corner and screeched in mindless fury. They charged them and were mowed down as well. Unfortunately, they had not noticed the infected security guard shamble over from one of the dark rooms and latch onto the agent, just as before. "Help me!" he yelled, but before any of the others could help, the guard released his spores onto the agent. Unexpectedly, they both collapsed to the floor. The group finished off the remaining infected and tensed for another attack.

"We're all going to die in here!" One of the other agents cursed, his arms shaking his rifle with fear.

Olivia grabbed the front of his Kevlar and glared at him. "Pull yourself together, agent!" She snapped. "You're a trained officer of Fringe Division! Start acting like one!"

"Y-Yes ma'am..." The agent blushed in embarrassment.

Lincoln had been trying to help the attacked agent, but it was no use. The man had inhaled the spores and his skin was already starting to develop rashes. It would most likely consume his whole body and mutate into something else in a few hours if he had to guess. "We can't help him right now, but we can make sure he stays put." Lincoln stood and looked around until he found what he was looking for. "These cables?" Lincoln walked over to the nearby wall, looking over the thick black cables that ran through an opening and was attached to a monitor. "We can use this to tie him up."

While one of the agents worked to disable that monitor, Lincoln looked the cables over for a good spot to safely cut them. "Do you know what you're doing?" Olivia asked quietly, not wanting to startle the other agents if his answer was less than optimal.

"Not a clue," he whispered back. "I'm a scientist and a detective... not an electrician..." he muttered, finding what he hoped was an already detachable section of the cable. "That's convenient," he smiled slightly and pulled gently. When the cables wouldn't budge he glanced at Olivia, who shrugged and nodded toward the cables, letting him know it was his prerogative. Lincoln took a breath and yanked the cables. They detached with a satisfying pop. Unfortunately, they were still attached firmly to the monitor. "Anyone have a knife?" He asked and thanked the agent that handed him what looked like a fancy multitool. Once they secured the cables around the unconscious agent, they pulled him to the room the infected guard stumbled out of. Making sure that no other surprises jumped out at them, they closed the door and prepared to head off once more.

They continued on their way through the labyrinth of corridors, dreading each step in that hellish maze, until they found more infected. To their relief, those poor people were already dead. Spotting something from the corner of her eye, Olivia bent down to one of the dead scientists and pulled out what looked like a blue key-card. "I haven't seen key-cards like these being in use in over a decade," Olivia passed it to Lincoln to look at.

Said agent studied the card. "Section D, priority access," Lincoln read aloud. "Maybe this leads to the answers we seek?" his brow rose.

"We're in section C right now..." an agent mentioned, then pointed to a monitor when the rest turned to him questioningly.

"We're also close to another security check-point. Since there are so many around here I bet you're right about that card, Linc'," Olivia said, glancing over to her partner. Lincoln smiled slightly, appreciating the nickname she slipped in. He had been wondering when she would start calling him that. "Let's go see if they have any useful stuff there," she motioned them to follow. When they got to the security room, they found a couple of dead, though uninfected people. One guard and one scientist. Olivia opened and locker and smiled, pulling out a rifle. "Here you go," she handed it to Lincoln who tested it for ammo. They also found a couple of environmental suits and masks. Unfortunately there were only three. One of the agents agreed to accompany them while the others agreed to monitor them from the security room.

They reached a pair of double doors at the end of the hall they were in and tried the car. It was a fit. With a resounding ping, the doors slid open. The smell of death was even stronger in that room, so strong in fact that it managed to make it through the filters of their masks. Fortunately for them, not a whisper of a soul remained alive in that room. Broken glass, equipment, blood of the floor, piles of grizzled bodies, but no threats otherwise. At the center of the room was a glass tank with what looked like a miniature garden.

"Those are not your typical flowers..." Olivia muttered in disgust. The "flowers" of the plants were fungal growths and the glass was shattered, brown dust all over the edges.

Lincoln picked up a bloodied tablet and read the contents, frowning at what he found. "Ophiocordyceps unilateralis..."

"What is it?" Olivia questioned, eying the agent with them as he kicked at the boot of one of the infected.

"It sounds familiar, but I'm not sure..."

"See, now, didn't you just say you were a scientist?" Olivia challenged playfully, trying to lighten the mood.

Her attempt worked a little. The corner of Lincoln's cheek twitched into what Olivia guessed was an attempt at a weak smile. Well that was something at least! You could never really get a serious Lincoln to lighten up, so this was a big step. "Sure, but I'm no floral expert," the bi-ocular agent explained, then set the tablet back down, his grim scowl back in place. "I think it's time to call Bishop with news. This is about as much as we'll get I think."

"There's nothing else on the device?" Olivia took the tablet and looked through it. She found data on that mystery fungus, but it might as well have been written in a different language. Olivia was by no means stupid, she just wasn't a scientist, she was a soldier. Given the proper education and time, she could figure this out like the best of them, but as it were, she had not been and there was limited time.

"There are some files with encryption on them. If I had more time I might be able to do something...-" there was that _time _word again, "-maybe, but I'm pretty sure there are other people more qualified."

"Like Astrid," Olivia offered with a smile. That girl could calculate her way into pretty much the seat of the world if given the opportunity and tools. "You're right though, it's time," she nodded and dialed Fringe HQ. When they got connected to Greg, they were patched into a conference call with Bishop. Olivia filled them in, explaining in detail everything that had happened, including finding the tablet with the name of the fungus.

Olivia was surprised when she heard clear worry in Bishop's voice. _"This is worse than I thought,"_ he said with an audible sigh. "_You need to secure a sample of the fungus, but refrain from killing any more people; I may be able to synthesize a cure if I am correct in my theory. The CDFC should be there shortly, make sure you have a sample ready."_

"And what about agent-" Lincoln was cut off.

"_Ah yes, your infected team-mate. Perhaps studying his infected blood will yield better results. I will inform the CDFC to extract him. Remember, do not kill anyone else,"_ Bishop firmly insister.

"Yes sir, but..." Olivia trailed off, glancing worriedly at her partner. Lincoln looked no better off.

"_I'm sorry agents, but you will have to wait until you are tested for infection before you can leave. I suggest you find a secure point and barricade yourselves until help can arrive,"_ Greg's grave voice told them next.

"Yes sirs..." Olivia sighed in defeat and once the call ended, followed Lincoln and the other agent out. "We should regroup with the others," she suggested. They made it to only a few steps from the security room before they heard the now familiar shuffle of infected feet.

Just as the mod of afflicted scientists were turning toward then, Olivia felt herself shoved into a small room. Lincoln pushed her a little deeper in and shut the door quickly. They heard the sounds of the other agents fighting off the afflicted people, screams of anger, fear, and pain echoed through the halls. Lincoln and Olivia looked at each other, a mirror look of worry in their eyes. Had they been seen?

When the sounds of violence faded away, Lincoln propped a broom across the door, securing it under the doorknob and stepped back. They waited a few minutes, but they only heard the dull sound of harsh breathing from the infected from somewhere on the other side of the door. There were no sounds of trying to get in or find them though, so they attempted to relax. They pulled their goggles off and tried to ignore the fact that they were now trapped. Olivia slid on the wall at the back of the utility closet and rested her head on her palm, her elbow propped up on a bent knee. Lincoln gave her an apologetic look but Olivia just smiled dismissively and shook her head. Sliding down next to her, Lincoln smiled back nervously and pulled his glasses out of his pocket, trying to distract himself by cleaning them.

In the end, they were forced to just sit and wait after all.

_**TBC...**_

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**End A/N: **What'll happen next? Tell me! Oh wait, I'm writing this, I already know! I decided to update rather quickly today because I was in a good mood and got a lot done. Let me know if you liked (or hated) it! Also, if you find a mistakes, please tell me so I can fix them!

**Chapter Theme:** Doom (movie) soundtrack.

Shout-Outs:

**zeusfluff**: Thank you for your input! Yeah, I tried to write a different Lincoln/Altlivia story than what's out there, though there are maybe one or two similar (short) stories on the same subject. I hope people are enjoying this...

**Jane**: I'm happy you're excited about this story! I hope you have a great time reading it!


	6. Treatment

**Days Gone By**

**Disclaimer: **I do not own Fringe, and I do not own the characters, but I do own this plot for this fan-based story.

* * *

Why hadn't they been attacked yet?

That was the question on both Olivia's and Lincoln's mind. The infected couldn't be that mindless that they couldn't open doors, right? They stayed perfectly still, perfectly quiet. They knew they were still out there, waiting for their next victim, they could hear the heavy breathing and low moans of pain from them. They knew that if just the two of them tried to fight off the horde, there was a strong possibility that they would be overwhelmed. Considering that each of those infected people could release spores at them, at any time, was too high a risk to take. Sure, they had hazmat suits with masks, but it would bar their vision and there was a chance it could be torn off. It was a calculated risk neither of them wanted to take.

So they waited, what more could they do?

Olivia rubbed her left palm with her thumb nervously, staring at the door. "We'll be fine..." Lincoln whispered. He glanced over at the door then, straining his hearing, but the whisper attracted no attention. They visibly relaxed a fraction and stole fleeting glances at each other, mutual looks of reassurance and at the same time, worry. If just one of them managed to hear them and find its way in...

"I know," Olivia shrugged. "It's just the waiting..."

"I know what you mean." Lincoln leaned his head back and shut his eyes. He opened them again when he felt Olivia flinch a little and looked down at her.

Olivia gave him a dismissive smile and shook her head. "It's nothing, I must have pulled something during one of the attacks," she rubbed her shoulder, close to her neck. Lincoln didn't remember seeing Olivia in any pain... until he shoved her in the closer. Had he done that and she was covering it up? Frowning guiltily, Lincoln reached over, putting his arm around her so he could reach the injured part on her right side and began to rub the spot rhythmically. Olivia said nothing, just closed her own eyes and let him. Sighing inwardly in relief from the pain, she leaned her head back against his arm. It was only when she felt him gently shaking her did she realize she must have dozed off. "Sorry..." she fought off a blush.

"It's okay, I just didn't think you'd want to sleep in the position... you might aggravate your neck more," Lincoln explained, his expression still a little guilty.

"Linc, it's okay," she assured him. "How long have I..?"

"Not long, about ten minutes," Lincoln shrugged.

"I'm sorry," Olivia cringed. He still had his arm around her, supporting her neck.

"I don't mind..." Lincoln responded with his own attempt to chase away a blush. Still he did not remove his arm. They were tense for a moment before Olivia decided she may as well get comfortable and slid a little closer to him, resting her head on his shoulder. Lincoln was surprised for a moment before he relaxed and let his hand rest on her arm. They remained this way for what seemed like hours more. If Olivia listened carefully and ignored the mutants outside their little refuge, she could hear the strong beat of Lincoln's heart. It was as rhythmic as his little massage was earlier. Thinking about it produced an unexpected fluttering sensation in her belly... since when did she get butterflies around Lincoln? Pushing the thoughts from her mind, she concentrated once more on the hypnotic sound of his heart.

It was only a few hours later when the CFDC finally arrived on the scene. Four black vans, two trucks carrying equipment and two sheriff patrol cars pulled up to the front. As people began to pile out, equipment was unloaded and perimeters were set. The police circled the facility, making sure there were no stragglers outside while the CDFC agents worked to set up blockades, tents, and screens. Once the forward base was set up, all the equipment in place and the satellite link to New York was established, a heavy set man with the show-me that gave him authority called in.

"This is Fringe, Major Cohen speaking," Greg answered his phone.

"_Good afternoon, sir. I am Malcolm with the CDFC. I presume you were made aware of our status in New Mexico?"_

"Yes. Are my agents secured?" Greg questioned, leaning forward on his seat to connect with the feed from the facility. According to the readings, there were still many signatures across inside the building. Unfortunately, he could not tell which heat signature belonged to his agents.

"_No sir, not yet," Malcolm answered._

"Alright. Bishop is on his way there and expects you to retrieve my infected agents. Agent Dunham said that he would be tied up in a closet near the main entrance."

"_Yes sir, we'll get on it right away." _Once the man had cut the connection, Greg dialed Olivia's earpiece. connecting Lincoln in on the call. He informed them of the situation and that it could take at least ten hours before help arrived, suggesting they try to get some rest.

Meanwhile, silence feel between Lincoln and Olivia once more. Lincoln could see the familiar poker-face slip onto Olivia's face, and he knew that it had nothing to do with their awkward sleeping arrangements. "What is it?" he asked her.

Olivia smiled fleetingly and shook her head as much as she could in her position. "It's nothing."

"I think I know you well enough now to tell when you're hiding something..." Lincoln craned his neck to look at her better.

The redhead laid her head back against him and smiled. It was ironic how she had thought she had missed the overly concerned and very perceptive part of her old partner. It seemed it was a very core 'Lincoln' trait. "This case, this situation... it reminds me of a case I worked with Frank on... a lot of people died," Olivia admitted.

"Frank, huh?" Lincoln said quietly. "Boyfriend?"

"Ex-fiance," Olivia clarified. "What? You jealous?"

"What's there to be jealous of? He's an ex now," Lincoln responded, if a little defensively.

Olivia paused for a second, wondering exactly what he meant by that, but decided it was useless thinking about that right now. She clicked her tongue and gave him an amused look instead. One thing was certainly true, that answer was about as Lincoln as an answer could get. "Anyway, we were stuck in a quarantine like this one except help didn't arrive in time... I just hope it will this time," she finished.

Lincoln remained silent for a while before finally taking a breath and revealing to her what had been bothering _him_. "I was once in a mission sort of like this too. Only, I was infected and could have died. It was a fungus too only this was had evolved into some sort of giant neural system."

"You're saying you were about to become part of the collective?" Olivia teased, throwing him a hopeful look. Had he seen Star Trek?

Olivia grinned when Lincoln all but rolled his eyes and smiled slightly. "It wasn't going to assimilate me if that's what you're asking. I could have died if it wasn't for Walter..."

"It's interesting that you'll now have both Walter Bishops that saved your life," the redhead smirked.

"I guess. That incident left me with uh, a few nightmares though..."

"Aww, don't worry, I'll hold your hand if things start to get too scary for you," Olivia teased with a mock pout.

"Shut up..." Lincoln blushed in embarrassment and bumped her shoulder with his playfully. "Speaking of nightmares. We should probably get some rest like Cohen suggested."

"I suppose," Olivia shrugged. "How do you want to do this?" She glanced around the small space they were in. "There's not exactly a whole lot of room to stretch out, and I'm not very fond of falling asleep sitting up like this," her nose crinkled.

"I could- we could..." Lincoln's ears turned pink. "I mean um, here-" Lincoln scooted forward until he was far enough up and then took his jacket off.

"What are you doing?" Olivia asked. Her heart was _not _speeding up from him just stripping his jacket off, damn it, it wasn't. She watched him bunch his jacket up and put it against the wall behind him before leaning back and using it as a pillow.

"Unless you want to... continue to be squished against the shelves... you could uh... I don't mind..." he stuttered, glancing away from her curious gaze.

"Lie on top of you?" Olivia grinned. On the outside she looked as relaxed as ever, but on the inside she could have sworn her stomach was doing somersaults. She just couldn't understand why she was affected by this so strongly. It was a sweet offer for her to be comfortable by a friend, it meant nothing at all! Still, she couldn't deny it; the idea of resting her head on his broad, shirt-clad chest was certainly appealing - even if he was still wearing his vest. Besides, what other option did she have? Resigning to her fate, though she didn't exactly fight it, she slid down and leaned back, rolling hesitantly over so that she was half-way on top of him. Olivia knew her heart was beating very quickly, but she found it comforting and, yes, endearing that his heart was racing just as quickly. Soon enough though, they both calmed down. Closing her eyes, she once again focused on the beautiful sound of his heart.

Walter Bishop had been having a full week this month. First, he had to create a task force to help clean up the amber mess after it was confirmed that there was no longer any danger, then he had to take care of legal matters concerning Agent's Lee's double, now he was eleven hours in his trip to New Mexico to fix yes another mess caused by the other universe. Ah, but he couldn't be angry at them so much anymore. After getting to know them, getting to know the other Walter, and finding how well he, in perhaps another time, had raised his son... the old scorn that had fueled his lust for revenge just wasn't in his anymore.

No, instead, Bishop found himself eager to handle these messes, because it meant just cleaning the way to a better future for all of them. He would miss the opportunity to see his son, but he had lived without the young man for more than twenty years, he could survive without him again. It was fortunate that the large helicopter he had ridden in was big enough to allow space and relative peace to sleep. Bishop found himself being woken by a shake on his arm. Looking up through sleep-hazed eyed, he noted one of the six Fringe troops standing over him with a pad. "Good morning, sir, we're about to arrive at the destination," he said, handing him the tablet.

Bishop wasted no time sitting up and taking the device. He cleared his throat of morning gruff as much as he could and gave the soldier a leveled look. "What is the status?" he asked, looking over the political cover for so much attention from the Secretary of Defense in an unmarked spot in New Mexico.

"CDFC agents obtained the infected agent and sedated him. Otherwise it had been a quiet eleven hours," the Fringe trooper answered.

"Good," Bishop nodded and looked down at the rapidly approaching land beneath the helicopter. Once they had landed, Bishop was directed toward his tent. He took note of quite a few baked goods and coffee on a table on the far end. Being as high up in status allowed Bishop certain comforts, coffee being one of them. Bishop ignored it for the moment in favor of assessing the situation he was presented with. While Malcolm, the head CDFC agent ducked inside and informed him of their status, Bishop observed the unconscious man carefully, taking mental notes on what signs presented themselves in the initial visual sweep. "Do you have the tools I requested?" Bishop finally turned to give the younger man his attention.

"I- yes sir, but why would you need-?"

"You need not trouble yourself with the processes of my work," Bishop dismissed him. "Thank you for the report, now, I must get to work." It took Bishop two hours to figure out exactly what happened to mutate the fungus and why it would affect a human in that way. Once he had his answer, he spoke to Malcolm once more, informing him what he would need to synthesize the cure. It was time he inform Major Cohen and his agents.

Back at the utility closet, Olivia stirred awake as he earpiece told her a call was coming in. Blinking sleepiness away she glanced over at the still asleep Lincoln. Studying him for a moment, she noticed that he looked more peaceful that she had ever seen on her old partner. A slight frown on his otherwise calm features reminded her that her phone was still beeping. "Lincoln, time he wake up," she pat his chest a few times. Lincoln jerked in response, his eyes opening in surprise to look over at her. Clearly his mind hadn't caught up with him yet and he forgot where he was and why she was tangled in his arms. Oh Olivia hadn't missed noticing his arm curled around her, holding her flush against him, she just firmly refused to acknowledge it. "Dunham," Olivia answered the phone, tapping Lincoln's ear to remind him that his was now beeping as well. Lincoln blinked in confusion for a few more seconds before quickly reaching his ear and connecting to the call.

"Lee here too," Lincoln answered. A pleasant shiver ran down Olivia's spine at the sound of Lincoln's rough-from-sleep voice. She had to try very hard not to let her imagination run rampant. Just what in the hell was wrong with her lately?

"_Agents, I'm relieved your alright," _they heard Greg's voice.

"We are, sir," Lincoln answered with a small flush of his cheeks, trying to ignore Olivia as she accidentally pressed against him in all the right places trying to sit up.

"_Agents. This is Walter Bishop. I have studied your infected comrade and come to the conclusion that you, Agent Lee, were correct. This fungus is a mutated version of Ophiocordyceps unilateralis."_

"What is that, sir?" Olivia asked curiously, swatting at Lincoln's hand when he tried to help her sit up. She slid off him, unable to stop her blush when he gasped. Oh, so he was _that _type of morning person. Scolding herself to focus, Olivia slid back against the wall and curled her legs to herself, giving him room to sit up as well.

"_Ophiocordyceps unilateralis is the fungus responsible for taking control of certain insects, most commonly ants. The fungus drives the ants to find a suitable spot for it to spread and grow. The ant eventually dies from the process. This is a mutated strand of it. I knew of a similar experiment being conducted, I just hadn't realized that the research had been developed so quickly." _Bishop responded.

"What were you trying to do?" Lincoln asked. He had finally managed to sit up and pulled his jacket over his lap, refusing to make eye-contact with the undoubtedly very amused redhead. Oh Olivia found this pretty entertaining alright. She had no idea how fun a flustered Lincoln could be to watch. But damn if she didn't recognize that she was a little bit flustered herself. It was a never-ending source of confusion and frustration for her. And not in the good way.

"_We were attempting to harness the ability the fungus has to control minds," _Bishop answered honestly. Lincoln and Olivia glanced at each other. Bishop hadn't even attempt to sugar-coat it. He had admitted in being part of an experiment to learn the means of mind control! _"I hadn't thought they would take the experiment this far, however. I'm not even sure of they deliberately infected someone of not. Believe me, human trials were never part of the equation. At least not like this. It was supposed to be a means to communicate in long distances,"_ Bishop sighed a little, pausing to collect his thoughts.

"What happened then?" Olivia asked with a frown.

"_It appears that the fungus has been spliced with human DNA, making it compatible with us. From what I can tell from your colleague, the normal antennae like protuberance the fungus on the ant has mutated the skin instead on its human host. From what I can see on his scans, the bacteria responsible for controlling the host appears to have infected a part of his parietal cortex. Many scientists, myself included, believe that the parietal cortex is the center of 'free will'... this is validated by the existence of the infection in this location,"_ Bishop explained. _"Fortunately, I believe with the proper stimuli delivered into the blood of the infected, a cure is very possible. I am very close to discovering what kills it. You will have to hold on for just a little longer."_

"Yes sir," Olivia answered, and the call was disconnected.

"So what now?" Lincoln asked softly.

"Now, we eat?" Olivia pulled out her energy bar that she hadn't touched the morning before. Lincoln patted his vest for a moment before finding his own. He smiled a little and joined her. The two spent the next two hours swapping horror stories, trying to ignore the fact that the morning chill from the desert the building sat in, was very quickly turning into smoldering heat. If, perhaps, they had been in a larger room, it might have not been so bad. As it were, the closet they sat in was not only _very _small, but the air flow of the AC was also switched off – to prevent the further spread of the fungus.

Olivia concentrated on playing the the reflection of her energy bar wrapper, trying to ignore Lincoln as he pulled his vest off and tossed his jacket to the side. Maybe he had the right idea though? Balling the wrapper and stuffing it in her pocket, Olivia pulled her own vest off, followed by her much loved black leather jacket. Olivia was glad that her shirt was a deep purple, not white like Lincoln's. She glanced up at him when he scratched his now two-day old scruff and smiled a tiny bit. He looked exactly like him now, no question about it. Lincoln had forgone wearing his glasses, tired of wiping the steam off of them and slipped them in his pocket. Without them on, his light beard growing in and his hair a complete mess, he might as well be Captain Lee.

"So," Olivia cleared her throat, trying to ignore the familiar, though now curiously duller pang of loss.

"So?" Lincoln was the one to lift a brow this time.

"I don't know," Olivia sighed miserably. "I'm bored," she shrugged.

"Me too," Lincoln smiled a little. They lapsed into awkward silence once more.

Two hours in that heat was enough to drive anyone to madness, but Olivia and Lincoln sat and waited patiently. As usual for her these days, Olivia's attention was once again drawn to Lincoln as he used his now slick with sweat arm to try to brush some from his forehead in vain. Olivia knew she was probably drenched herself, but at the moment her attention was caught by the tiny beads of sweat trailing down her partner's neck, disappearing into his... now pretty see-through shirt. Tearing her gaze away Olivia mentally kicked herself, at once angry with herself and at a loss. There had to be a reason why she was suddenly to entranced by Lincoln Lee. She tried to remember if she ever thought of her old partner that way, but honestly it was all a blur. Perhaps because when Lincoln had been her partner, she had had other men in her life to keep her distracted. "I hope a cure is developed soon..." Olivia muttered. She had to get away, had to clear her mind, organize her thoughts.

Meanwhile, Walter walked with the team of Fringe troops that had arrived with him, explaining where to administer the successfully synthesized cure. It had to go directly into the Carotid artery, the fastest and largest vein closest to the brain. The team was instructed to tranquilize all infected they encountered, administer the cure, and find the missing team. The team leader turned his gas-mask enveloped head toward the secretary and saluted him. "Don't worry, sir, we'll do our very best," he told him in a muffled voice.

"See that you do," Bishop nodded and gestured for them to carry on. The soldiers swept into the building with efficiency, knowing what to expect and how to deal with the situation. It took them half an hour to quickly move through the complex, spending no more than half a minute in each room and not bothering to wait after they hosed down infected people before moving on. They found the survivors and the other agents, still locked in the monitor room, telling them to sit tight until they finished.

"I think I hear someone," Lincoln mentioned, turning his head to the door. They heard a loud cry of rage then, just outside their door, followed by the unmistakable sound of tranquilizer darts and bodies collapsing. "This is Agent Lee, Agent Dunham and I are in here!" Lincoln called, offering his hand to help Olivia up as he stood. Once one their feet, they opened the door carefully. Finding six Fringe soldiers outside the door was a great source of relief.

"It's good to see you both unharmed," one of the soldiers mentioned. "Agent Lee, Agent Dunham, we were instructed to tell you to secure the survivors and head out to be scrubbed down," he explained.

"Right, thank you," Olivia said, literally pushing Lincoln out the door and toward the hall. "Come on, I want to get out of here already," she told him.

"Alright already..." Lincoln muttered, though he was not at all upset. The sudden loss of her hand on his arm almost made him trip. She had removed it as though burned. Glancing back at her, he could have sworn she had seen her blush before she brushed past him.

"Pick up the pace, slow-poke," she simply said. Figuring it was just his imagination, Lincoln jogged after her. It didn't take them long at all to find the remaining agents and the survivors, including a few other survivors they had not met on their initial run. Guiding them out, Olivia and Lincoln stepped out into them, while veiled by the screens, sunny outdoors. The CFDC was on them before they could blink, instructing them where to go to get cleaned, to strip of clothes, and to hold still. After Olivia and Lincoln were scrubbed clean and in fresh clothes, they were treated to a lunch of sandwiches and coffee - courtesy of the good Secretary of Defense - while Bishop explained what would happen now. It would take a few hours to a day for the cure to take effect and then they would sterilize the facility. When he was done, Bishop ordered they return home, their job there was complete. He would take care of the rest.

"Will you be okay here sir? Do you need anything else?" Olivia asked curiously.

Bishop's normally severe mouth twitched into a small smile. "A benefit of being in a high position allows me to clear my schedule at a moments notice. Thank you for asking though. Go on, take the jet back to HQ. I'll be fine here." Lincoln and Olivia couldn't argue with a direct order from the Secretary of Defense to go home! They both felt like they could do more to help, but honestly they were much to exhausted to be of much help anyway. The ride back to New York was in silence, but this time comfortable. Sweet, sweet cool air conditioning and fluffy seats nearly lulled them into blissfully relaxed sleep aboard the comfortable plane, despite having woken up from a good twelve or so hours of sleep just a few hours ago. They did not speak all that much during the ride, too lost in their own tangled thoughts, processing everything that had happened to them in those three days.

When the jet landed in Richard Nixon International Airport, they felt relief once more. Lincoln would never get tired of how amusing the different names of what was familiar places to him were. JFK Airport was now RN Airport. Once they got to Fringe HQ, the sun had already began to slip below the horizon. Greg listened to them as they tiredly gave their report, trying to stay awake as they did. Before Lincoln could finished explaining the scientific ramifications Bishop's experiments could have on their society, Greg dismissed them, telling them to go home and sleep. They were dead on their feet. After what felt like a long week, Lincoln and Olivia were very glad to be in their beds, even if one of them was a hotel bed.

_**TBC...**_

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**End A/N: **Seems like things are starting to get interesting between them, eh? Olivia is swimming in de nile river. This chapter was _meant _to be a short one... funny how things work out.

Shout-Outs:

**Guest**: You're welcome!

**Castlefringereader**: Something tells me you want more?


	7. The Stone Man

**Days Gone By**

**Disclaimer: **I do not own Fringe, and I do not own the characters, but I do own this plot for this fan-based story.

* * *

Compared to the hectic three days he endured last week, Lincoln had been having a pretty slow and easy week this time around. Surprisingly, besides a mission to stop a terrorist stealing tech from HQ, there hadn't been too many more cases. That hadn't stopped him from training whenever he could though. He had already read five books relating to that universe. He read a political, military, cultural, historical, and a trivia book Olivia insisted on. He was pretty sure his studying wouldn't be done in a while though, since it seemed whenever he finished a book someone brought him a new one. He didn't really mind, he enjoyed reading when he needed to know all he could about his new universe.

Aside from reading, Lincoln, with the help of Olivia, had been going through rigorous exercises to get as fit as a Fringe agent on this side had to be. It had been almost two weeks since he started the regime and he was _just _starting to feel a difference. Mostly pain though. Still, it was nice looking in the mirror and approving at the subtle changes! Their routine was simple, they'd work until the evening, exercise in the gym, head home to wash up, and then meet up again at "their diner" to relax before going to sleep. Once or twice Lincoln had been invited to watch movies at Olivia's apartment. He never stayed too long.

Most mornings Lincoln would wake up more or less refreshed and prepare for the day. But sometimes... sometimes he would have familiar nightmares. Sometimes they were of exceptionally bizarre cases he had worked on, and other times they were of the loss of his own friend and partner. That morning was one such morning. In his dream Robert would suddenly sit up on the table, surrounded by the other bodies, who would turn their sheet covered heads to watch. With his flesh still translucent, still very much dead and choking to speak, he would point at him, blaming him for his death, for not trying hard enough. Lincoln shook himself awake. He pushed himself off the bed and leaned over at the edge, taking deep breaths to calm himself down. Dreams such as these had been bothering him since he first stumbled onto Fringe Division back in his old universe. Putting it out of his mind, Lincoln got up and prepared for the day.

The day had gone by as quietly as it had been that week. There had been a few more cases, but nothing quite as intense as the infested laboratory in New Mexico. By the end of the day, Lincoln met Olivia at "their diner" after showering at the hotel after his exercises. He sat at "their booth" and waited for her to arrive. Pulling out a newspaper, or news_pad_ as they were called here, since they were essentially very thin, almost see-through tablets, he browsed through it. He found the crossword section, smiling at the fact that despite how different some things were, others didn't seem to change much at all. At least he didn't need a pen anymore.

Olivia had just finished taking a long hot shower. She stepped out of the steamy room and began pulling her clothes on. As she did, she thought of how much her new partner threw himself into learning all he could about his surroundings, including working very hard to refine his fitness. It was commendable but honestly something she had expected from him. At his core, Lincoln was the same person no matter what universe or time-line he came from. She had tried very hard not to compare both of them so much, and it _was _getting easier those days, but little things like that seemed to halt her in her steps. Olivia would become both confused and hopeful. Lincoln was both a different person and the same person at the same time. He _was Lincoln, _but with different memories, choices, and a slightly different personality. He was like an identical twin, but more. These thoughts would spur very weird dreams in her, though for some reason the ones involving him or both of them were not quite that easy to remember. She wondered what that meant.

Once Olivia was done preparing, she forced the confusing thoughts from her mind and left her apartment to meet up with her friend. Fortunately, HQ was relatively close to her apartment, so the drive didn't leave her mind much time to wander too far. Walking into the diner she found her partner working on his crossword puzzles as usual. She smiled affectionately and plopped down at the seat in front of him. "Hey, 'Liv," Lincoln said without looking up.

"Good one today?" Olivia questioned, peering over at the puzzle.

"Yeah, I'm getting pretty good, I think! All that studying is paying off," he looked up at her then, a toothy grin gracing his scruffy features. Lincoln had stopped clean-shaving after Olivia told him that if he wanted to make people believe he had more confidence, he had to look like he wasn't constantly trying to impress someone. Leaving a bit of scruff on his face meant he was relaxed and not bothered in what others thought. Personally though, Olivia just missed the bit of fuzz on his cheeks, -not that she'd tell him that. She still wasn't sure if he'd puff up like his counterpart had. Lately he _had _been relaxing more. Besides, she was sure what also helped him in his decision to keep the fuzz was when she scratched him that one time. He hadn't been having a good night's sleep and when he started to scratch at his beard in what she thought was a stress-tick, she reached over, swatting his hand away, and all-but caressed his cheek. Lincoln had gone dead still, his eyes widening a fraction, but let her scratch his cheek. She had honestly enjoyed helping him too, and hadn't thought of it any other way. Thinking back on it now though... she wondered what he was thinking. She wondered what _she _was thinking too, she'd never done that for the other Lincoln before. "'Liv?" Olivia blinked back to reality and realized she had been staring at him.

"Yeah?" She asked, forcing herself to focus once more.

"I asked if you think I'll be ready for my reevaluations next week?"

"Of course! You're much stronger than you were before, and like you said, the studying is paying off!" Olivia answered with a friendly grin. It was true, if it wasn't for that universe's techniques and equipment to quickly built muscle and endurance up, it might have taken Lincoln several months to get to the place he was at now. They talked for a bit, mentioning the weird cases and how odd that there hadn't been too many of them lately.

"Don't jinx it, 'Liv," Lincoln smiled.

"What? The really strange ones are entertaining at least," she grinned back.

Lincoln nodded in reluctant agreement before smiling at the waitress who handed him his drink. Olivia glanced over at the girl and saw her wink at her partner. She rolled her eyes and smirked. Her old partner would have caught on immediately and flirted away, even with her there, but this Lincoln just turned back to give her his attention. Though she was hesitant to admit it to herself, Olivia found herself enjoying this "new him" quite a bit lately. She refused to think about what that could mean. "Was the one you tease Charlie about really as strange as I heard?" Lincoln asked suddenly, snapping her out of her thoughts.

"The one with the mutated spider monster? Yeah, that one was _crazy_," Olivia nodded, glad for the distraction. "See, it started out with these kids, college students most likely, 'animal rights activists', breaking into a research lab and freeing the animals. There was this room in the back, sealed with a large metal door. They must have been curious or something because they opened it and were immediately attacked. The survivors of the attack fled the scene and tried to escape but it must have tracked them. The next morning we were called in to investigate their deaths."

"That sounds really similar to that one case back in my old universe. I studied their Fringe files too and your description matches a very similar incident. It must be the same case both Charlies got their parasites. Go on," Lincoln was interested now. It was a probably never ending quest of his to compare both universes, see what choices people made to find themselves in their respected circumstances. And honestly, watching her describe things all actively, using her hands and expressive eyes was always really quite fascinating to him too.

"Right so we get there and there is the car they had used to escape in, flipped over and mangled, like really torn into. The bodies of the victims were laying out with various marks on them. We couldn't figure out what kind of animal would leave the type of marks either, especially the very large double fang marks. Charlie had joked it was a vampire, but the wounds were full of paralyzing poison. Turns out it was a hybrid creature of many different animals and insects. The main insect used was an arachnid. It's intent was to paralyze its victim, make it host for its young so they could eat their way out and spread out that way..." Olivia made a look of disgust.

"Ugh, that somehow sounds worse than the other case," Lincoln shuddered.

"Charlie had the bright idea to track it after... your counterpart, pieced together the animals and found clues. We went after it and found it trying to search for a suitable nest. In a park of all places. It attacked Charlie, pulling him up a tree. We had to shoot at it seventeen times before it released Charlie, but it had been too late. Charlie had been injected with the thing's young."

"You said the things were in his blood, right? Why not swap it out?" Lincoln suggested.

Olivia frowned in confusion. "What do you mean?" She heard of blood transfusions, but this would be... wait. "Do you mean a dialysis?"

"Yeah. Just remove the contaminated blood while replacing it with new blood of his type?"

"That would work if the spiders didn't start to react and grow with such a drastic change like that. If Charlie were to attempt to do that, maybe in little steps, it might work, but it would take God knows how long. Not to mention the cost of the procedure and availability of that much blood," Olivia explained. "I think he just prefers to take his injections. Fringe Division pays for it and he only has to take it once or twice a day," she shrugged. "Who knows, he might do a transfusion one day."

"So what happened to it?"

"Well, it escaped after we got to Charlie but we later found it trying to make a home in a sewer system. We had to poison it to death because regular bullets weren't doing a whole lot of damage to it," she finished.

Lincoln sat and thought for a while. "...You're right, that _was_ weird," his cheek twitched into a familiar smile. Not quite the dimples yet, it'd probably be a while before he unleashed those bad boys at her. Olivia had thought on many occasions with her old partner that his smiles should have come with warning labels. They finished their drinks and bid each other a good night, neither realizing how much the other didn't quite want to separate just yet.

The next morning, Olivia woke with a start when her phone went off. How such a little device such as the earpiece could make such a racket was beyond her. Fitting it to her ear she answered the call. _"Dunham,"_ it was Greg Cohen. _"There has been a Fringe case. Get over here,"_ he said.

"Sir?" Olivia yawned.

"_You have half an hour, agent,"_ Greg disconnected the call. So much for no cases lately! Taking a moment to stretch, Olivia kicked her covers off and snatched her fresh clothes from her dresser on the way to her bathroom. It took her sixteen minutes to finish showering, six more to throw on clothes, thirty seconds to grab a piece of fruit, and fifteen to drive to work. She wouldn't be exactly on the amount of time her boss wanted her there by, but whatever. Stepping into Greg's office, she was greeted with Greg handing her a pad with the case.

Looking over the pad made her both cringe and peak her curiosity. "Stone people?" Olivia crinkled her nose at the odd title, a twinkle of amusement in her eyes as she flipped through the report. People were... turning to stone? "You're not serious?"

Instead of answering directly, Greg Cohen went on with the mission debriefing. "Earlier today the body of a homeless woman was found by a delivery man. The forensics team say they've never seen anything like it; most of the woman's body was turned into solid bone by an unknown source, though evidence of a struggle found on her, including that of multiple needle marks suggest a person was involved."

"Who could have done this?" Olivia's eyes widened a fraction. "Is it even possible?" Okay, so that was a stupid question. In her line of work she was met with the impossible all the time – or _improbable,_ if you asked Astrid.

"That's what you and Lee will be finding out today, agent. Find out what happened and whoever or _whatever_ did this," Greg told her. One could never be quite sure if it was a 'who' or and 'what' in the Fringe. He caught the question in her eyes. "Secretary Bishop feels Mr. Lee is due for a test. If he does well in this mission, he may be granted his title back."

"That's great!" Olivia grinned, bouncing on her heels.

"Indeed," Greg nodded, placing his folded hands over the desk. "I called him in on the case a bit before you. He is probably on his way to the site. I suggest you go on your way as well."

"Yes sir," Olivia turned on her heel and moved out. She took the time it took to get to the site to eat her fruit, wishing for a good ol' cup of coffee, and hoping it would be more accessible in the near future. It didn't take long to get the street, finding the line of Fringe SUV's and general police cars all piled into the little alley. She moved her own car in and parked it. Stepping out she found Lincoln crouched over the body of the poor woman, his detective mode firmly in place as he studied the body. "So what's the skinny?" She asked him, kneeling down on the other side of the body.

"You jinxed it, that's what," Lincoln said simply, without even looking over at her.

"Sorry," Olivia grinned and shrugged.

"No you're not," Lincoln finally glanced up at her, over the edge of his glasses and smiled back. "Anyway," he brushed himself off and stood up, waiting for her to finish looking over the body as well. "Meet Clara Brown, she had no family, no home, lost her job a few months ago due to lay-offs. A package delivery guy found her laying here, half-hazardly tucked in the corner a few hours ago. Forensics found a few messy set of prints on her, most likely accidental. Otherwise by the marks and residue on the body it would appear as though she had been handled by latex gloved hands."

"A mad scientist?" Olivia suggested with an amused smirk.

Lincoln shrugged and pulled off his glasses to rub his eyes slowly. "Your guess is as good as mine."

"You okay?" Olivia stood, giving him a look of concern. She had noticed his weariness as he spoke, but she had figured it was because he had been here for a few hours already. It _was _pretty early in the morning, after all.

"Sure," he shrugged again. "Bad dreams, I guess."

Olivia smiled sympathetically. "I know how you feel. I get them too."

"Cases like these don't help much," Lincoln sighed, slipping his glasses back on. "Your counterpart once told me that it would get easier."

"Has it?" Olivia questioned, leaning out of the way when a police officer jogged by, probably being called away to another crime scene. She hadn't noticed she leaned almost directly into Lincoln to get out of the way. Lincoln certainly had though! As she pushed slightly forward, trying to dodge the cop, Lincoln was presented with a very nice view of her cleavage from where her top buttons on her shirt were left unbuttoned. He could smell the fruity scent of her shampoo, was that peach? Since when did they make peach scented shampoo? Lincoln would have to try to find and personally thank whoever invented it, because on her? Mixed with the little bit of scent that made up Olivia Dunham, it was about the most pleasing smell he'd had all month. When she turned back to look at him, he had turned away from her quickly, hoping his blush was not that noticeable.

"Erm, yeah I suppose," Lincoln cleared his throat awkwardly. "In the moment, I guess I'm not so bothered by these cases... but at night..."

"I guess I can understand that," Olivia nodded. "_That _will get easier too though. At least, it will become more manageable." Olivia and Lincoln rode back to HQ with the incomplete prints, hoping the team there would be able to match them. Astrid told them an elaborate set of probabilities and percentages that they would be able to find the man responsible, or that it could simply be the delivery man's prints when he found the body. "I guess we'll just have to wait!" Olivia mentioned, sliding into her seat.

Almost two hours later, they finally got the results. "The prints belong to Dr. Eric Anderson," Lincoln read the file on the overhead screen out load. "A geneticist – or _ex _geneticist – who had been a project leader in Genspace*, working on cures for various genetical problems. He has a daughter who has 'fibrodysplasia ossificans progressiva'. Her leg was turning to bone. The pain was so bad that she slipped into a coma."

"What's ...fibro...dysplasia ossificans progressiva?" Olivia tested the scientific word and frowned, not liking how she pronounced it.

"Otherwise known as 'Stone Man Syndrome'," Lincoln began, "if I understand correctly, it's an impossibly rare genetic disease that effects the connective tissue – muscles, tendons, ligaments. They slowly turn to bone over a period of time. It is often mistaken for cancer, since on the scans there appear to be solid growths where otherwise healthy tissue is supposed to be," he explained.

"So you can just... have it and start turning into bone?" Olivia shook her head, feeling both pity for the man and understanding for how crazy he seemed to have become if evidence pointed to this being _caused _by him. No doubt he was trying to find a cure for his daughter, but this was taking it too far, experimenting of others. He had to be stopped.

"No, it's typically a result of the body's natural healing mechanism. A simple fracture, even a sprain could bring it on. They can't even remove the 'infected' bone because that just causes even more bone to grow over the injury. Anderson's daughter had broken her leg during a soccer game, which spurred it on." Lincoln switched the screen off and turned to her. "I'd say he's our best lead in this. Any luck finding him?"

"I have been attempting to find Dr. Anderson's location since the prints came in positive for his DNA," Astrid explained. "So far his show-me has not been reported for four months. Aside from sending drones to try and locate Dr. Anderson, he will be difficult to find. Would you like me to tell you the statistics?"

"No, that's okay," Olivia smiled at her. "What do you think, Linc?" She turned to her partner, who blinked in surprise. Not so much for the nickname, as she had started calling him that more and more since that mission to New Mexico. No, he was just a little surprised that she'd ask his opinion. Not that she hadn't before, she had, but it felt like more than that somehow.

Lincoln resisted the urge to point at himself incredulously. "You're asking me?" He was glad that he no longer sounded as insecure as he had before. All the same, he had been used to _her _giving the orders and trailing him around. Not that he'd mind the opportunity for a bit more responsibility!

"It's time for you to take the lead on some missions," Olivia told him.

"Um, well, okay then," Lincoln straightened slightly. "In that case, I'd like to go back to the scene, talk to people to see if there were any witnesses and see from where Ms. Brown could have been deposited."

"Sounds good to me! Lead the way," Olivia grinned, gesturing with her hand for him to head out first. Lincoln smiled slightly before moving out. It took them half a day to find a single witness, describing a blue van with chipped off paint in the back grabbing the described woman off the streets two days ago. Following the lead, they reached a market place where a fish vendor explained the same blue van moving back and forth through the street over the course of a few months. Deciding they were close, Olivia and Lincoln continued searching on foot until they found a suspicious "abandoned" warehouse, the locks of the garage door obviously torn off. Slipping inside silently, they finally found the van inside. Knowing they were in the right spot, they crept onward.

Elsewhere, Dr. Eric Anderson stood over his latest test subject, strapped to an examination table, ignoring the pleads to let him go. He had found this homeless man out in the streets after depositing his latest failed experiment. The man had been so desperate for food and warm shelter for the night that he had gone with him no questions asked. Eric figured who would miss him? Who would miss any of the homeless people 'polluting the streets'? Certainly not him. If it meant saving his little girl. So he used the excuse over and over to justify his actions: "I'm sorry, I'm doing this for her," was all Eric said, flicking the needle of a syringe to test its flow. He tuned out the cries and please from the man, firmly believing that a few more tests and he would find a cure for his precious daughter.

Eric had not heard the footsteps of the approaching agents, all he heard was the blood rushing in his ears, voices telling him it was for the greater good, and his test subject's incessant wailing. He _did _however hear the soft click of a bullet being loaded into the chamber of a pistol. "Fringe Division! Drop the syringe and put your hands up!" Olivia demanded. Eric's eyes widened in surprise, not having expected the authorities to find him so quickly. Clearly he hadn't covered his tracks well enough!

"No need for that, agents... I'll cooperate..." Eric said softly, putting the syringe down slowly before putting his hands up. He noted the female agent talking to someone on her earpiece, most likely calling in backup. He had to act soon.

"Don't try anything..." Lincoln said, approaching cautiously. Eric took a calculated risk, hoping the agent in front of him had lowered his guard even a little. "Stop!" Lincoln shouted when the man took off. "Take care of the victim!" he called after Olivia as he ran. Olivia hadn't had to be told twice, she had already been trying to see how much the mad scientist had victimized him. Unfortunately, it seemed as though the man had been injected quite a few times already without whatever genetical altering stimuli he had been given.

"Try not to move, help is on its way..." Olivia said as gently as she could.

"There- there's no help for me! I... I can feel it move through my bo-body!" The man said through clenched teeth and tear-stained cheeks. Olivia watched in horror as the man's leg began to solidify. What could she do? What could anyone do? Lincoln had said there was no cure for this!

Meanwhile, Lincoln slid to a stop when he encountered several tall rows of shelves filled with various machinery and dusty boxes. He slowed down, his pistol at the ready as he crept through the maze. It was impossibly dark there, despite the old hanging lights above his head that swung back and forth with the wind. The moving lights sent shadows shifting, making his tense. Lincoln controlled his breathing, using it to steady his movement as he made his way down a row. The man could be anywhere. The sudden shift of a large shadow had Lincoln turning sharply toward it, expecting the crazed man to jump out at him.

Eric Anderson _had _jumped out, but what Lincoln didn't know was that what he saw was the bent shadow from the swinging lights, not the silhouette of the man himself. There were three things that came to Lincoln's mind then, as he was thrown to the floor. One, he underestimated the desperation of this man. Two, he was now in a tremendous amount of pain. Three, his whole right side was covered in blood. Falling to the floor with a gasp, Lincoln turned to see Anderson standing over him with a bloodied knife. "I'm doing this for her! For my baby girl! It's all for her! I can't lose her!" The man screamed at him. Lincoln reacted before he thought, having seen the man move a split second toward him before he tore his gun from the floor and fired.

Bang! Bang!

Olivia covered the now dead victim with an old wrapping sheet when she heard the gun fire. She took off, hoping the man hadn't had a gun, hoping Lincoln had fired first. Skidding to a halt, she found the man collapsing to the floor with a screech of pain. Lincoln was on the floor, gun raised toward the man, a steady pool of blood forming near him. "Linc!" Olivia ran over to him, kicking the man's knife out of his hand and leaning over her partner. "That's a lot of blood there, buddy," she whispered, her teeth clenched in worry.

"This? Naw, it's nothing..." Lincoln muttered, not realizing it was exactly what his double had said before he died. He realized his mistake too late, seeing Olivia's eyes widen in horror. "Seriously though, I'm losing blood but I don't... I don't think he got me anywhere vital?" He winced, realizing how stupid that excuse sounded.

"You're not a doctor, Linc, just shut up and keep putting pressure on the wound a second," Olivia ordered. She went over to the ex-geneticist, noting the bullet holes on both his knees. Damn, every version of Lincoln seemed to be a pretty good shot. She took out her cuffs and unceremoniously and rather violently forced the man over to fit it over him. She told him his rights, anger and fear clear in her tone despite hiding it from her face. When she was done, she went back to Lincoln and helped him with his wound, calling it in. Fortunately, she had called for help a while ago so it only took them about seven minutes to make it there.

Olivia saw to it that the man was immobilized, patched so he wouldn't bleed to death either, and taken to the transport vehicle. When she was done, she had enough time to watch Lincoln being taken into the ambulance. She wouldn't stay behind this time. Cohen could get his report after she made sure her partner was going to survive this time! And so she followed the ambulance in her car, her fingers tightly clutching the steering wheel. Olivia was not allowed in the surgery hall, so she resorted to pacing in the hall outside of it, worry marring her usually controlled emotions. The only thing she could think at that moment, was a repeated mantra of "not again".

When the doctor stepped out half an hour later with an unreadable expression, Olivia felt herself begin to hyperventilate. _"I'm sorry, Agent Dunham. Captain Lee... didn't make it." _Those damn words that the soldier had told her were haunting her thoughts then. "Agent Dunham?" The doctor queried.

"Yes. How is he? Agent Lee- is he..?" Olivia bit her lip and raked her hand through her red tresses.

"Agent Lee is fine," the doctor explained quickly. Olivia said nothing, just let out a breath of relief, feeling suddenly weak. She braced herself on the wall closest to her and listened as the doctor explained. Lincoln had been right after all. The knife hadn't penetrated anything vital, no arteries and no organs. It was a clean muscle stab. Fortunately the man who stabbed him had had steady hands even then, little damage otherwise was done to the surrounding tissue.

"We sealed his wound but he will need to apply nanite-wraps every three hours," the doctor explained. "He is being instructed by the nurse on what to do, but I am confused, agent. Hadn't Agent Lee been admitted here before under more serious conditions? He should know how to apply nanite-wraps..."

"Agent Lee had recently undergone a... drastic operation... I'm sorry, that is all I can say. Any more is classified," Olivia explained. Clearly this hadn't been the doctor that treated her old partner for his... bullet wound. The doctor didn't need to know that the 'operation' was that fateful mission.

"I see. Anyway, he should be out in a few minutes. As I told him, he will be sore for the next week until the nanite-wraps can finish fully healing him," he warned her.

"Thank you doctor," Olivia nodded. She sat down in the seats lining the hall and let her head drop onto her hands. She closed her eyes and thanked every deity she could think of. Not five minutes later, the doors opened once more, revealing a nursing wheeling Lincoln over in a wheel chair.

Lincoln saw the guilt and worry written all over his partner's face and gave her a leveled stare. "Hey," he said softly, catching her eyes with his. "It was _not _your fault, 'Liv," he said firmly. Olivia seemed to blink in confusion. "It's written all over your face," he explained.

"Oh," Olivia gave him a hint of a smile and shrugged. "I could have been there," she said simply. "I should have gone with you."

"I told you to stay behind. It was my call," Lincoln told her firmly. "Come on, we should report to Cohen," he said dismissively, not wanting to hear Olivia belittle herself any more. Olivia thankfully didn't argue and took over wheeling him out. She helped him into the car. The Department of Defense Hospital was only five minutes away from Fringe HQ so they rode in silence. When they got there, Greg stood from his chair, surprised to find Lincoln in such rough shape. He had been informed of the situation, but he hadn't thought it was this bad. Lincoln took point once more, explaining the mission and how he got stabbed.

"It's unfortunate you were injured, Agent Lee," Greg said gravely. "I hope you take comfort in knowing you helped stop a mad man."

"Yes sir," Lincoln nodded.

"How would you like your title back, agent?" Greg asked as he sat down.

"I'm sorry?" Lincoln blinked in surprise.

"Secretary Bishop had been informed of the mission success before you two got here. He has agreed to 'take care of the paper work', so long as you keep training. Is that agreeable to you, agent?"

"Y-Yes sir!" Lincoln answered, befuddled and elated. Olivia beamed at him, not surprised... so she knew? "You knew of this?"

"Yep! Congratulations, partner!" She grinned happily at him.

"Yes indeed. Congratulations Agent Lee. It is good to have you officially on board," Greg smiled. "Now, I suggest you go and get some rest. You're back on as an Agent, but your wound will keep you from going on any missions that require too much movement. Your shuttle is waiting for you whenever you are ready," he informed him. Lincoln winced, not liking the idea of being taken off of most cases like that. He understood, though, and agreed. "You injury won't excuse you and Agent Dunham from paper work, however. I expect to see you both tomorrow, agents."

"Yes sir..." they both answered in defeat. There was never any escaping the paperwork!

_**TBC...**_

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**End A/N: **"Genspace" is an actual biology lab in New York. This was _also _going to be a short chapter!

**Chapter Theme: **Placebo – Running Up That Hill

Shout-Outs:

**Guest: **You're welcome!

**Jane:** I'm glad you love it! I generally like to communicate with my readers, especially when they leave feedback!


	8. Adapting

**Days Gone By**

**Disclaimer: **I do not own Fringe, and I do not own the characters, but I do own this plot for this fan-based story.

* * *

_Olivia found herself in an mercilessly familiar place in time. She stood by, unable to do anything as her partner approached with the informer. As before, she could not stop herself from trying to save him... but it was no use. As before, he walked right into the shooter's sights and down her went. Olivia felt tears prick her eyes as she rushed to him. Maybe she could save him this time? Maybe she could find a way to safely remove the bullet? But before she could even reach him, her surroundings vanished. She found herself in Fringe headquarters again, looking at a map of the supposed shapeshifter signals. Looking around her, she began to panic when she did not see her latest partner. "Lincoln?" she called._

"_Ma'am?" Olivia turned to see the familiar solider approaching with bad news. "I'm sorry. Lincoln Lee didn't make it."_

"_...You mean Captain?" Olivia's heart began to beat erratically._

"_No, ma'am, neither of them made it..."_

Olivia shot up in bed, eyes wide, breath short, and heart smashing itself against her ribcage. Olivia clutched the front of her shirt, trying in vain to calm herself, or at least slow down her wild pulse. She resisted the impulsive, illogical urge to call Lincoln to make sure he was okay. Olivia yanked the covers off her and went to splash her face with water. Bracing herself on the bathroom counter, she took deep breaths to steady herself and forced the dream to retreat as she always did. It had been a few days since Lincoln's knife wound, but still, the scare of almost losing _him as well_ nearly gave Olivia conniption. After a few minutes, the dream faded away and she relaxed.

When Olivia got to work that day, Lincoln was at his desk, diligently working on the latest bit of paperwork for the few light cases he had been allowed to work on. She could see the frustration of being forced to sit behind clear on his face. Olivia wouldn't know what to do if she were in his position. They carried on the day without incident – no cases that day! That evening, as they were logging off to head home, Olivia decided it was time she made good on her offer to help Lincoln with something when he had asked almost a month ago. She walked over to his desk and leaned on it slightly. "You asked me if I could help you get an apartment a while ago, tomorrow is our day off, why don't we do that then?" She hoped he hadn't made any plans, but maybe she should have asked a while ago and planned it better. She was never one to plan so far ahead, always ready for action on the spot.

"Thanks! That sounds great," Lincoln smiled cheerfully. Clearly he was tired of living in a hotel, one could _only_ imagine _why_!

"Hey, look, I'm sorry it took me so long to help you find an apartment," Olivia began, "I didn't realize our lives would get so busy! And then you got hurt and I didn't want to risk further-"

"It's okay!" Lincoln interrupted. "I get it. I'm all better now and we have the chance to go apartment shopping."

"Alright, great! In that case, why don't you get your things and stay at the spare room at my place tonight? That way we can head off on the apartment hunt ASAP?"

Lincoln fought off a blush and tried to smile nonchalantly. "Sure, that sounds good," he made to shrug but it ended up looking more like he was trying to scratch his ears with his shoulders... He kicked himself inwardly for being such a wuss and cleared his throat to inspire confidence in his voice. "I don't have much so it shouldn't take more than five minutes, just let me finish up here."

Since the trip to the hotel and then to Olivia's apartment was rather absurdly quick, they didn't speak much on the way there. Stepping inside, Olivia tossed her very loved black leather jacket on a chair and gave Lincoln the tour. Her apartment was pretty big for the location she lived in, most likely having used considerable influence to get it. She had a medium sized kitchen, with a table in the center for meals, two bedrooms, two full bathrooms – one in the master room, the other in the hall, and a rather large living room. All in all it was a pretty sweet setup.

Lincoln's brow hiked up when he saw how empty her fridge was, but Olivia managed to pull out some bread, peanut butter, and jam. Not the best of meals, but it made for a pretty tasty dinner anyway. "Sorry, Frank used to do all the shopping... I usually don't have a whole lot of time," Olivia had said. Lincoln hadn't responded, just looked around and imagined what it must have been like for Frank to live with her. Grocery shopping wasn't such a huge deal for Lincoln, that idea in mind he felt envious of Frank for having been able to be with Olivia in that capacity. Chasing away another blush, Lincoln returned his focus to Olivia as she spoke about how she didn't really spend a whole lot of time at home. Their conversations slipped into random topics until they both realized they should probably go to sleep. The odd sort of tension between them helped them in that decision.

Things would have gone just fine if Lincoln hadn't stepped out of the guest room to grab another blanket from the linen closet. On his way back he had noticed Olivia's door open a crack. The reflection on the mirror displayed her getting undressed. He spotted her silky black undergarments and spun around, tearing his gaze away. Oh he wanted to keep watching, a deep and intense drive inside him told him he was a moron for not continuing... but damn it, he was better than that! He wasn't sure what his double would have done, but he resisted the temptation and forced his feet back toward his room. He knew his dreams would be full of her tonight... but if he was being honest with himself, when he wasn't having nightmares, he dreamt of her anyway. Only this time, he had vivid images to go along with his fantasies.

Olivia hadn't been as chivalrous that night.

When she stepped out of her room to grab a glass of water, she had been presented with a similar opportunity. She wasn't so quick to look away however, though she made sure he didn't catch her staring. She told herself that she was only checking to see how his wound was healing, nothing else... but she knew that despite her true curiosity for that, she had never had the opportunity to look at her partner in that fashion. She couldn't deny that she liked what she saw. His skin was starting to tighten with muscles in all the right places, a shadow of an athletic form starting to develop. A little more training and he'd be statue-worthy. Brushing away her increasingly inappropriate thoughts, she _did_ take note of the wound spot too; not even a tiny sliver of a scar left on his skin, as far as she could tell from the distance she stood from him at least. When he began to turn, face her where the bed was, Olivia slipped quietly back into her room.

As she lay in bed, Olivia wondered why she was suddenly so fascinated by him? Could losing a version of him once already opened her eyes to him? Or had she always felt a tug toward him that she ignored, for the sake of their continued healthy friendship? And then she thought of something else... she had heard him walking around a little earlier, and she kept her door open a crack as well... could he have done the same thing? Strangely enough, the thought of him seeing her didn't bother her at all.

One thing was for sure, neither of them managed to get too much sleep that night.

Lincoln had not been expecting to see Olivia already awake when he woke up as early as he had that morning. Olivia sat in the living room, tea cup in hand, looking over her tablet. She moved her eyes up at him from her tablet when he shut his door. "'Morning," she smiled. "The kettle is still hot if you want some tea."

"Um, thanks, not much of a tea drinker though," Lincoln said quietly.

"Neither was he at first." Lincoln knew who she was talking about and nodded in acceptance. He'd probably have to get used to it too until the coffee trees were restored... if they ever were. The blight had done a number on wildlife. Even though it was true that it no longer existed, thanks to the other universe healing that one, it was still tricky, expensive, and time consuming trying to terraform the ruined landscape. "You're welcome to orange juice though, we still have plenty of that -thank God!" She grinned.

Lincoln smiled back, "thanks," he said as he made his way to the kitchen. Last night during "dinner" he had felt nervous and awkward, but for reasons he couldn't explain he now felt a little more at ease. In fact, it almost felt natural to wake up to her in the morning... even if they hadn't shared a bed. Brushing those thoughts from his mind, and glad that Olivia couldn't see his blush, Lincoln set out to get himself some juice.

What Lincoln hadn't known was that a similar thought had been on Olivia's mind since she opened her eyes in bed that morning. Lincoln, the other one, had crashed once or twice at her place before, but it was usually either he was trying to escape a persistent date, or he and Charlie had too much fun at the bar that night. Her house was much closer to the bar they frequented before than his, after all. But this... it felt different. _He_ was different. In many ways, and Olivia was having a hard time reconciling this.

A few minutes later, Lincoln walked over with a cheerful little smile. "You went shopping?" He mentioned.

"Yeah, there's a gas station nearby that's open twenty-four seven, I figured I'd be a good hostess and offer you some breakfast at least," Olivia smiled, pleased that he seemed happy about this. A meal of eggs, fruit, and toast was a big improvement from the pb&j dinner they had had last night. She took her tablet with her and led him back to the kitchen, setting it on the counter. "I assume you like eggs too?"

"Love them!" Olivia was surprised and oddly very happy to see Lincoln's face split into a familiar grin, brandishing those two glorious dips in his cheeks and all.

"So the saying is true then? The way to a man's heart really is through their stomach!" Olivia laughed.

"I suppose..." Lincoln rubbed his neck in slight embarrassment, though he couldn't keep a ghost of that smile from his lips. He hadn't had eggs in what seemed like months now. "Here, let me help you-"

"No, no, it's fine! I got it, you're a guest!" Olivia insisted, though she knew that it wouldn't work – every single Lincoln in any universe seemed driven to be stubborn.

"It's the least I can do," Lincoln responded just as firmly. This, however, led to a few complications. Olivia had been used to working with Frank in the kitchen; they knew where to move and when to stay out of each others ways. Lincoln and Olivia were not quite in sync quite yet.

"Yet?" Olivia muttered to herself as she tried to dodge Lincoln reaching for another cup for her.

"What's that?" Lincoln glanced over at her as she tried to evade him. Unfortunately, as he turned she tried to move to the side, but this only led to them bumping into each other. "Sorry..." Lincoln murmured, smiling nervously.

"'S alright," Olivia waved his apology away, glad he had gotten distracted enough. "Er, here, you move here," Olivia placed her hands on his shoulders – surprisingly firm shoulders, nudging him aside so she could get around him to the fridge. She ducked away from him quickly to hide her irrational sudden fluster.

"Maybe I _should _just get out of your way?" Lincoln mentioned, he too blushing slightly.

"Well now you're committed to helping! Here," Olivia handed him the carton of eggs. As they cooked they fell into a more efficient rhythm, though the tension between them just seemed to escalate with every bump and graze of their arms or fingers. Neither of them knew what was wrong with them, but both of them breathed an inward sigh of relief when they were done and seated at the table. When they were finished, Olivia sat down next to him and showed him what she had been looking over that morning. There were several listings for apartments relatively near Fringe Headquarters, at decent prices, and she had selected the ones she thought he would like best.

"Looks good, I like this one the best from the images," Lincoln leaned over to show her. Olivia blinked in alarm at how her heart seemed to pick up speed just a little more when he did that. Insisting to herself that it was probably the sugar from the orange juice, she focused on what Lincoln was saying instead... and not on how long his eyelashes were, or how soft his lips looked, or how unreasonably nice his eyes were... Olivia physically shook her head, mentally berating herself for thinking such things. This was _Lincoln_! He wasn't even her type! ...Was he? Well, then again, she went for the "nice guys" ...her old partner put on a show that sometimes bugged her, hiding how he felt behind brashness and flirting with every woman he could... but her new partner didn't do that. He _was _a "nice guy", and she'd be a fool and blind not to admit he definitely did have looks going for him. That she always knew. She was glad that so far he hadn't flaunted it like his alternate had. "'Liv? You still with me?"

"Wha? Oh, yeah I am, hey why don't we get started?" Olivia grabbed his plate and hers and took them to the sink, finding his very close proximity suddenly overpowering. Olivia used the silence of the car ride to calm down. Funny, this sort of thing hadn't happened to her since she was in the academy, crushing on the older soldiers. Then Frank came along and she experienced it again... she hadn't felt this way with "her other Lincoln", so why now?

When they got to the first apartment, one that resembled Lincoln's counterpart's, they noticed a few things off about it right away. It was too far from work, too close to a bad neighborhood, and a little more expensive than it had been listed at in the advertisement. That didn't stop the landlord, a sweet little old lady, from trying her best to negate the negatives. When Lincoln and Olivia tried to speak to each other in private to see if they should reject the offer or not, the landlord must have been eavesdropping for she said:

"Well isn't this sweet? You two must be a couple!" The little old lady smiled brightly. Lincoln and Olivia stared at each other awkwardly, noticing just then how close they were standing.

"No... no ma'am, we're just friends..." Olivia corrected her, taking a slight step away from him. Olivia hid her astonishment at noting the very quick flash of disappointment that went through Lincoln's face. She decided it was the lighting in the room. Surely he wouldn't want..? This would happen once more, prompting Olivia to retaliate by agreeing that they _were _a couple. Kinky lovers looking for a fun place for their role-playing mystery nights. Of course, both Lincoln and the landlord gave Olivia a startled look. Olivia took Lincoln's arm and fluttered her eyes playfully.

"I um... well," Lincoln flushed scarlet. "We're not-"

"So what more is there to see from this place?" Olivia interrupted, winking at Lincoln. She was pleased when his gave her a subtle roll of his eyes but kept quiet. Maybe a little fun would help loosen him up a bit? The landlord showed them the rest of the apartment, while – to Olivia's amusement – he kept stealing awkward glances at them. By the end of the day, not only had the finally found a good deal, but Lincoln had started to relax and play along a little.

"Oh look, dear, we can keep our toys here..." Lincoln had said, pointing to a built-in shelf in one of the rooms.

"On display too, I like how you think honeybun," Olivia grinned. The look the landlord had given them was almost too much. Keeping their laughter in was almost difficult by that point. Once the paperwork was finished and the first payment given, Lincoln was handed his new keys.

"Why does it seem like you're more invested in finding the perfect place than I am?" Lincoln asked. Olivia simply grinned and shrugged as she always did. After spending one more night at Olivia's apartment that weekend, they took advantage of the fact that there didn't seem to be any sudden cases to go shopping for basic essentials for Lincoln's apartment. On their way back to the car, totting almost two carts full of items, Lincoln felt his glasses slip off his nose. He tried to swipe at them quickly, catch them before they fell, but he was not quick enough. "Damn!"

"What's wrong?" Olivia looked over to see Lincoln picking up his cracked glasses.

"I left my old ones back... well, back in the other universe," Lincoln sighed.

"You could always get your eyes fixed? There aren't a whole lot of people with glasses around here... I sometimes where them but mostly as magnifiers," Olivia suggested. It took a bit of convincing, and assurance that Olivia would be fine seeing him looking so much like her old partner, but finally Lincoln agreed. Fortunately, he had been paid recently for the latest case and had enough for the surgery. One hour later, Lincoln stepped out wearing shaded protective eyewear. "How'd it go?" Olivia asked him.

"It's done, but I have to wear this for another half hour until my eyes adjust," he explained. Once that was done, Olivia offered to help straighten some things out in his apartment, figuring he'd be able to relax and get to sleep in his place faster if they both worked. By the time they unloaded the bought items into his new apartment, Lincoln's eyes had returned to normal and he was able to put the shades away. Olivia smiled wistfully at him.

After helping him set up his new stuff at his place, though a bit more subdued than before, Olivia decided to turn in early. "I'm beat. I'll see you tomorrow, Linc..." she said. She wasn't really that tired, but she needed time to sort through her thoughts, understand what it is she really feels about this. Sure, it was her idea to get his eyes fixed, but she had assumed that somehow he would look differently, she knew it was stupid, but perhaps it was some sort of defense mechanism.

"Alright," Lincoln sighed inwardly, having a good idea as to why she was heading home so early. "'Night, 'Liv."

_**TBC...**_

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**End A/N: **I'm sorry for the wait, life sucks sometimes! Things are starting to get interesting between them, eh? One of the reasons for the wait is because I had to completely change the next two chapters. I had been starting to write in a soap-opera-y way and that had to be fixed immediately! For a while I didn't know what to write though, but I finally figured something out. Just to warn you, I have some exams coming up so I'm not sure when the next chapter will go up! Please let me know what you thought!


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